Molecular markers linked to disease resistance in soybean

ABSTRACT

The present invention relates to methods and compositions for identifying, selecting and/or producing a soybean plant or germplasm having a Rps1 resistance allele and resistance to Phytophthora sojae. A soybean plant, part thereof and/or germplasm that has been identified, selected and/or produced by any of the methods of the present invention is also provided.

CROSS REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/000,388 filed Jan. 19, 2016, which is a continuation of U.S.application Ser. No. 13/486,705 filed Jun. 1, 2012, which claims benefitof U.S. Provisional Application No. 61/492,104 filed Jun. 1, 2011, thedisclosures of which are incorporated by reference herein in theirentirety.

STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, submitted under 37 C.F.R. §1.821, entitled 9207-48PR_ST25.txt, 15,619 bytes in size, generated onMay 9, 2011 and filed via EFS-Web, is provided in lieu of a paper copy.This Sequence Listing is hereby incorporated by reference into thespecification for its disclosures.

FIELD OF THE INVENTION

The present invention relates to compositions and methods foridentifying, selecting and producing Phytophthora resistant soybeanplants. More particularly, this invention relates to markers that areassociated with a particular region of Chromosome 3 of Glycine sp.(previously called Linkage Group (LG) N), which is associated withresistance to Phytophthora sojae, can be used for producing soybeanlines with improved resistance to P. sojae.

BACKGROUND

Soybean (Glycine max L. Merr) is a major cash crop in North America andaround the globe. Soybean oil is one of the most widely used edibleoils, and soybeans are used worldwide as animal feed and for humanconsumption and for industrial purposes. P. sojae is an oomycetepathogen, which was first described in Ohio and shortly thereafter inIndiana and North Carolina (Suhovecky and Schmitthenner, Ohio Farm HomeRes. 40:85-86 (1955)). P. sojae has now been reported to be present inall soybean growing regions of the U.S. as well as other parts of theworld (Zhang et al. MPMI. 19(12):1302-1310(2006); (Wrather et al. Can.J. Plant Pathol. 23:115-121 (2001)). Symptoms of Phytophthora Root Rot(PRR) caused by P. sojae include yellowing and wilting of leaves andbrowning of lower stems and branches (Demirbas et al. Crop Sci.41:1220-1227 (2001)). PRR is the second leading cause of yield loss insoybean in the United States. In 1998, yield losses due to PRR, in theU.S. and Argentina, the top soybean producing countries, were 1149 and92 thousand metric tons respectively (Id.). PRR results in annualworldwide soybean crop losses of $1 to $2 billion (Zhang et al. MPMI.19(12):1302-1310(2006)).

To date, eight loci, Rps1, Rps2, Rps3, Rps4, Rps5, Rps6, Rps7, and Rps8,have been identified which provide race-specific resistance to P. sojae.These loci were mapped to chromosomes 3, 16, 13, 18, 18, 18, 3 and 13(previously called molecular linkage groups (MLG) N, J, F, G, G, G, N,and F, respectively) and simple sequence repeat (SSR) markers werereported to be linked to these genes (Burnham et al. Crop Sci.43:101-105 (2003)); Diers et al. Crop Sci. 32:377-383 (1992); Gordon etal. Crop Sci. 46:168-173 (2005); Gordon et al. Phytopathology 97:113-118(2007); Lohnes and Schmitthenner, Crop Sci. 37:555-556 (1997); Sandhu etal. Genetics 168:2157-2167 (2004); Sandhu et al. J. Hered. 96(5):536-541(2005); Weng et al. J. Hered. 92:442-446 (2001)).

The Rps1 locus is complex having multiple alleles including Rps1a,Rps1b, Rps1c, Rps1d, and Rps1k (Bernard and Cremeens, Soybean Genet.Newsletter 8:40-42 (1981); Lohnes and Schmitthenner, Crop Sci.37:555-556 (1997); Ferro et al., Crop Sci. 46:2427-2436 (2006); Weng etal. J. Hered. 92:442-446 (2001)). Rps1a was mapped on chromosome 3(previously called MLG N), flanked by SSR markers, Satt159 (0.7 cM) andSatt009 (3.2 cM) (Weng et al. J. Hered. 92:442-446 (2001)). Therecombination value was reported to be 0.16 and 0.13 between the geneRps1 and Satt159 and Satt152 in another research (Demirbas et al. CropSci. 41:1220-1227 (2001)). Additionally, Satt530 and Satt584 were alsoreported to be linked to Rps1, Rps1b, and Rps1c with recombinationvalues of 0.00 and 0.00, 0.12 and 0.20, and 0.14 and 0.21, respectively(Id.).

Rps1-k, first identified in the cultivar Kingwa (Bernard and CremeensSoybean Genet. Newsletter 8:40-42 (1981)), has been used extensivelyused gene in breeding Phytophthora-resistant soybean cultivars(Schmitthenner et al., Plant Dis. 78:269-276(1994)). High resolutiongenetic and physical maps have been constructed for the Rps1-k region,and the gene has been isolated through positional cloning andtransformation experiments and its sequence has been published inGenBank with the accession EU450800 (Bhattacharyya et al. Plant Mol.Biol. 34:255-264 (1997); Gao et al. Mol. Plant Microbe Interact.18:1035-1045 (2005); Kasuga et al. Mol. Plant Microbe Interact.10:1035-1044 (1997)). Although previously Rps1-k was considered to be asingle gene, two functional units/genes, Rps1-k-1 and Rps1-k-2 werecloned from the Rps1-k locus. Rps1-k-1 is located between 17988 bp to21677 bp and Rps1-k-2 is located between 42421 bp to 46170 bp of theGenBank accession EU450800. The Rps1-k gene sequences are disclosed inU.S. Pat. No. 7,256,323B1 to Bhattacharyya et al.

Currently, the presence or absence of Rps1 alleles is determined byphenotyping against different races of P. sojae in the greenhouse. Thus,the present invention overcomes the shortcomings in the art by providingmarkers associated with the different Rps1 alleles, thereby allowing fora more precise and faster characterization of soybean cultivars for thepresence or absence Rps1 alleles by molecular analysis rather than bymore time consuming greenhouse phenotypic analysis.

SUMMARY OF THE INVENTION

Compositions and methods for identifying, selecting and producingsoybean plants having Rps1 resistance alleles are provided. Soybeanplants and/or soybean germplasms and/or parts thereof having Rps1resistance alleles are also provided.

Accordingly, in one aspect of this invention, a method of identifyingand/or selecting a soybean plant or germplasm having an Rps1 resistanceallele is provided, the method comprising: detecting, in a soybean plantor germplasm, the presence of a genetic marker associated with an Rps1resistance allele, wherein said genetic marker comprises (1) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ); (2) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ); (3) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ); (4) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ); (5) an A allele at nucleotide 251 of SEQ ID NO:6(SY2724BQ); (6) an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(7) an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (8) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele atnucleotide 251 of SEQ ID NO:2 (SY2721AQ); (9) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ) and a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ); (10) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ);(11) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), and a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (12) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (13) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and a G allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (14) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (15) a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (16) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (17) wherein the SNP is an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (18) is a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(19) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (20) an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (21) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (22) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (23) an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(24) an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (25) a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (26) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (27) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (28) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (29) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (30) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (31) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (32) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ), (33) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (34) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(36) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a Callele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (37) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (39) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (41) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (46) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide 251 of SEQID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above, thereby identifying and/orselecting a soybean plant or germplasm having an Rps1 resistance allele.The genetic markers (e.g., SNPs, combinations of SNPs) of the presentinvention are associated with the Rps1 resistance alleles Rps1-a,Rps1-c, Rps1-k, or any combination thereof.

In other aspects, the present invention provides a method of producing asoybean plant having an Rps1 resistance allele, the method comprising:(a) detecting, in a soybean germplasm, the presence of a genetic markerassociated with an Rps1 resistance allele, wherein said genetic markercomprises (1) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ);(2) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (3) a Gallele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ); (4) an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ); (5) an A allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (6) an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (7) an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (8) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and a C allele at nucleotide 251 of SEQ ID NO:2 (SY2721AQ); (9) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a G allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ); (10) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ) and a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ); (11) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), anda G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (12) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), and a G allele at nucleotide 251 of SEQID NO:8 (SY2725AQ); (13) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (14) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (15) a Callele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (16) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (17) wherein the SNP is an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (18) is a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(19) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (20) an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (21) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (22) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (23) an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(24) an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (25) a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (26) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (27) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (28) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (29) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (30) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (31) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (32) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ), (33) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (34) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(36) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a Callele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (37) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (39) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (41) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (46) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide 251 of SEQID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above; and (b) producing a soybean plantfrom said soybean germplasm, thereby producing a soybean plant having anRps1 resistance allele.

A further aspect of this invention provides a method of introgressing anRps1 resistance allele into a soybean germplasm that is lacking the Rps1resistance allele, the method comprising: (a) crossing a donor parentalsoybean line comprising a genetic marker associated with an Rps1resistance allele with a recurrent parental soybean line that lacks saidmarker to produce progeny; (b) selecting progeny comprising said markerand backcrossing said progeny with the recurrent parental soybean line,wherein said progeny are selected by detecting, in their genomes, thepresence of said marker associated with an Rps1 resistance allele,wherein said marker comprises: (1) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ); (2) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ); (3) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ);(4) an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (5) an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (6) an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (7) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (8) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:2(SY2721AQ); (9) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (10) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ); (11) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), and a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (12) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), and a G alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (13) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ) and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(14) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (15) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(16) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (17) wherein the SNPis an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (18) is a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (19) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (20) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(21) an A allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (22) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (23) an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (24) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (25) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (26) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (27) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (28) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (29) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (30) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (31) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (32) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ), (33) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (34) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (36) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(37) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(39) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(41) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (46) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above; (c) backcrossing the selectedprogeny of (b) with the recurrent parental soybean line to producefurther progeny; and (d) repeating steps (b) to (c) one or more times,thereby introgressing the Rps1 resistance allele into the recurrentparental line, and thus introgressing the Rps1 resistance allele intothe soybean germplasm that is lacking the Rps1 resistance allele.

Compositions comprising a primer pair capable of amplifying a nucleicacid sample isolated from a maize plant or germplasm to generate amarker associated with an Rps1 resistance allele are also provided. Suchcompositions may comprise, consist essentially of or consist of one ofthe amplification primer pairs and/or probes identified in Table 1.

These and other aspects of the invention are set forth in more detail inthe description of the invention below.

DETAILED DESCRIPTION

All technical and scientific terms used herein, unless otherwise definedbelow, are intended to have the same meaning as commonly understood byone of ordinary skill in the art. References to techniques employedherein are intended to refer to the techniques as commonly understood inthe art, including variations on those techniques or substitutions ofequivalent techniques that would be apparent to one of skill in the art.

All patents, patent publications, non-patent publications and sequencesreferenced herein are incorporated by reference in their entireties.

Disclosed herein is the identification and design of genetic markers(SNPs and/or combinations of SNPs) that can be used to identify allelesassociated with P. sojae resistance in soybean.

Therefore, present invention provides compositions and methods foridentifying, selecting and/or producing soybean plants having one ormore Rps1 P. sojae resistance alleles. In addition, the presentinvention provides soybean plants and/or soybean germplasm having withintheir genomes one or more SNP markers associated with one or more Rps1resistance alleles. These SNPs are located within an approximately 1.7megabase (MB) region of Glycine sp. Chromosome 3 (Linkage Group N).

Definitions

Although the following terms are believed to be well understood by oneof ordinary skill in the art, the following definitions are set forth tofacilitate understanding of the presently disclosed subject matter.

As used herein, the terms “a” or “an” or “the” may refer to one or morethan one. For example, “a” marker (e.g., SNP) can mean one marker or aplurality of markers (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 and the like).

As used herein, the term “and/or” refers to and encompasses any and allpossible combinations of one or more of the associated listed items, aswell as the lack of combinations when interpreted in the alternative(“or”).

As used herein, the term “about,” when used in reference to a measurablevalue such as an amount of mass, dose, time, temperature, and the like,is meant to encompass variations of 20%, 10%, 5%, 1%, 0.5%, or even 0.1%of the specified amount.

As used herein, the transitional phrase “consisting essentially of”means that the scope of a claim is to be interpreted to encompass thespecified materials or steps recited in the claim and those that do notmaterially affect the basic and novel characteristic(s) of the claimedinvention. Thus, the term “consisting essentially of” when used in aclaim of this invention is not intended to be interpreted to beequivalent to “comprising.”

As used herein, the term “allele” refers to one of two or more differentnucleotides or nucleotide sequences that occur at a specific locus.

A “locus” is a position on a chromosome where a gene or marker or alleleis located. In some embodiments, a locus may encompass one or morenucleotides.

As used herein, the phrases “pathogen resistance locus” and “pathogenresistance gene” refer to loci and/or genes that have been associatedwith pathogen resistance as defined by the markers disclosed herein. Insome embodiments of this invention, these loci/genes are present onGlycine sp. Chromosome 3 (Glycine linkage group N), and linked to themarkers represented by SEQ ID NOs: 1-8. Similarly, the phrase “pathogenresistance phenotype” refers to a phenotype the expression of which isinfluenced by a pathogen resistance locus and/or a pathogen resistancegene.

As used herein, the terms “desired allele,” target allele and/or “alleleof interest” are used interchangeably to refer to an allele associatedwith a desired trait. Disclosed herein are exemplary genetic markers(SNP alleles) that are associated with soybean plant resistance orsusceptibility to P. sojae. For example, the SNP alleles can beassociated with Rps1-c, Rps1-a, Rps1-k, or a combination thereof. Insome embodiments, the “desired allele” will depend on the gene that isbeing assayed (e.g., Rps1-a, Rps1-c, Rps1-k or combinations thereof).Thus, for example, when assaying for Rps1-c, the desired allele atSY2726DQ is A. In contrast, when assaying for Rps1-a or Rps1-k, thedesired allele at SY2726DQ is C. In a further example, when assaying forRps1-a, the desired allele at SY2724AQ is G. In contrast, when assayingfor Rps1-c, the desired allele at SY2724AQ is C. In a still furtherexample, when assaying for a combination of Rps1-a and Rps1-c, thedesired allele at SY2724AQ is C. Alternatively, when assaying for acombination of Rps1-a and Rps1-k, the desired allele at SY2724AQ is G.

A marker is “associated with” a trait when it is linked to it and whenthe presence of the marker is an indicator of whether and/or to whatextent the desired trait or trait form will occur in a plant/germplasmcomprising the marker. Similarly, a marker is “associated with” anallele when it is linked to it and when the presence of the marker is anindicator of whether the allele is present in a plant/germplasmcomprising the marker. For example, “a marker associated with a Rps1resistance allele” refers to a marker whose presence or absence can beused to predict whether and/or to what extent a plant will displayresistance to one or more races of P. sojae.

As used herein, the terms “backcross” and “backcrossing” refer to theprocess whereby a progeny plant is crossed back to one of its parentsone or more times (e.g., 1, 2, 3, 4, 5, 6, 7, 8, etc.). In abackcrossing scheme, the “donor” parent refers to the parental plantwith the desired gene or locus to be introgressed. The “recipient”parent (used one or more times) or “recurrent” parent (used two or moretimes) refers to the parental plant into which the gene or locus isbeing introgressed. For example, see Ragot, M. et al. Marker-assistedBackcrossing: A Practical Example, in TECHNIQUES ET UTILISATIONS DESMARQUEURS MOLECULAIRES LES COLLOQUES, Vol. 72, pp. 45-56 (1995); andOpenshaw et al., Marker-assisted Selection in Backcross Breeding, inPROCEEDINGS OF THE SYMPOSIUM “ANALYSIS OF MOLECULAR MARKER DATA,” pp.41-43 (1994). The initial cross gives rise to the F1 generation. Theterm “BC1” refers to the second use of the recurrent parent, “BC2”refers to the third use of the recurrent parent, and so on.

As used herein, the terms “cross” or “crossed” refer to the fusion ofgametes via pollination to produce progeny (e.g., cells, seeds orplants). The term encompasses both sexual crosses (the pollination ofone plant by another) and selfing (self-pollination, e.g., when thepollen and ovule are from the same plant). The term “crossing” refers tothe act of fusing gametes via pollination to produce progeny.

As used herein, the terms “cultivar” and “variety” refer to a group ofsimilar plants that by structural or genetic features and/or performancecan be distinguished from other cultivars/varieties within the samespecies.

As used herein, the terms “elite” and/or “elite line” refer to any linethat is substantially homozygous and has resulted from breeding andselection for desirable agronomic performance.

As used herein, the term “P. sojae-resistant soybean plant or germplasm”refers to a soybean plant or soybean germplasm that is capable ofresisting infection by P. sojae. When used in reference to germplasm,the term refers to the ability of a plant that arises from thatgermplasm to resist infection by P. sojae.

A “genetic map” is a description of genetic linkage relationships amongloci on one or more chromosomes within a given species, generallydepicted in a diagrammatic or tabular form. For each genetic map,distances between loci are measured by the recombination frequenciesbetween them. Recombination between loci can be detected using a varietyof markers. A genetic map is a product of the mapping population, typesof markers used, and the polymorphic potential of each marker betweendifferent populations. The order and genetic distances between loci candiffer from one genetic map to another.

As used herein, the term “genotype” refers to the genetic constitutionof an individual (or group of individuals) at one or more genetic loci,as contrasted with the observable and/or detectable and/or manifestedtrait (the phenotype). Genotype is defined by the allele(s) of one ormore known loci that the individual has inherited from its parents. Theterm genotype can be used to refer to an individual's geneticconstitution at a single locus, at multiple loci, or more generally, theterm genotype can be used to refer to an individual's genetic make-upfor all the genes in its genome. Genotypes can be indirectlycharacterized, e.g., using markers and/or directly characterized bynucleic acid sequencing.

As used herein, the term “germplasm” refers to genetic material of orfrom an individual (e.g., a plant), a group of individuals (e.g., aplant line, variety or family), or a clone derived from a line, variety,species, or culture. The germplasm can be part of an organism or cell,or can be separate from the organism or cell. In general, germplasmprovides genetic material with a specific molecular makeup that providesa physical foundation for some or all of the hereditary qualities of anorganism or cell culture. As used herein, germplasm includes cells, seedor tissues from which new plants may be grown, as well as plant parts,such as leaves, stems, pollen, or cells that can be cultured into awhole plant.

A “haplotype” is the genotype of an individual at a plurality of geneticloci, i.e., a combination of alleles. Typically, the genetic loci thatdefine a haplotype are physically and genetically linked, i.e., on thesame chromosome segment. The term “haplotype” can refer to polymorphismsat a particular locus, such as a single marker locus, or polymorphismsat multiple loci along a chromosomal segment.

As used herein, the term “heterozygous” refers to a genetic statuswherein different alleles reside at corresponding loci on homologouschromosomes.

As used herein, the term “homozygous” refers to a genetic status whereinidentical alleles reside at corresponding loci on homologouschromosomes.

As used herein, the term “hybrid” in the context of plant breedingrefers to a plant that is the offspring of genetically dissimilarparents produced by crossing plants of different lines or breeds orspecies, including but not limited to the cross between two inbredlines.

As used herein, the term “inbred” refers to a substantially homozygousplant or variety. The term may refer to a plant or plant variety that issubstantially homozygous throughout the entire genome or that issubstantially homozygous with respect to a portion of the genome that isof particular interest.

As used herein, the term “indel” refers to an insertion or deletion in apair of nucleotide sequences, wherein a first sequence may be referredto as having an insertion relative to a second sequence or the secondsequence may be referred to as having a deletion relative to the firstsequence.

As used herein, the terms “introgression,” “introgressing” and“introgressed” refer to both the natural and artificial transmission ofa desired allele or combination of desired alleles of a genetic locus orgenetic loci from one genetic background to another. For example, adesired allele at a specified locus can be transmitted to at least oneprogeny via a sexual cross between two parents of the same species,where at least one of the parents has the desired allele in its genome.Alternatively, for example, transmission of an allele can occur byrecombination between two donor genomes, e.g., in a fused protoplast,where at least one of the donor protoplasts has the desired allele inits genome. Offspring comprising the desired allele can be repeatedlybackcrossed to a line having a desired genetic background and selectedfor the desired allele, with the result being that the desired allelebecomes fixed in the desired genetic background. For example, a markerassociated with a Rps1 resistance allele may be introgressed from adonor into a recurrent parent that is not resistant to P. sojae. Theresulting offspring could then be repeatedly backcrossed and selecteduntil the progeny possess the Rps1 resistance allele(s) in the recurrentparent background.

As used herein, the term “linkage” refers to the degree with which onemarker locus is associated with another marker locus. The linkagerelationship between a molecular marker and a phenotype may be given asa “probability” or “adjusted probability.” Linkage can be expressed as adesired limit or range. For example, in some embodiments, any marker islinked (genetically and physically) to any other marker when the markerssegregate from each other in the next generation less than 50% of thetime, less than 25% of the time, less than 20% of the time, less than15% of the time, less than 10% of the time, less than 5% of the time,less than 4% of the time, less than 3% of the time, less than 2% of thetime, or less than 1% of the time. Thus, in some embodiments, two lociare linked when they are separated by less than about 50, 40, 30, 25,20, 15, 10, 5, 4, 3, 2, 1, or 0.5 map units or centiMorgans (cM).

As used herein, the phrase “linkage group” refers to all of the genes orgenetic traits that are located on the same chromosome. Within thelinkage group, those loci that are close enough together can exhibitlinkage in genetic crosses. Since the probability of crossover increaseswith the physical distance between loci on a chromosome, loci for whichthe locations are far removed from each other within a linkage groupmight not exhibit any detectable linkage in direct genetic tests. Theterm “linkage group” is mostly used to refer to genetic loci thatexhibit linked behavior in genetic systems where chromosomal assignmentshave not yet been made. Thus, the term “linkage group” is synonymouswith the physical entity of a chromosome, although one of ordinary skillin the art will understand that a linkage group can also be defined ascorresponding to a region of (i.e., less than the entirety) of a givenchromosome.

A centimorgan (“cM”) or a genetic map unit (m.u.) is a unit of measureof recombination frequency and is defined as the distance between genesfor which one product of meiosis in 100 is recombinant. One cM is equalto a 1% chance that a marker at one genetic locus will be separated froma marker at a second locus due to crossing over in a single generation.Thus, a recombinant frequency (RF) of 1% is equivalent to 1 m.u.

As used herein, the term “linkage disequilibrium” refers to a non-randomsegregation of genetic loci or traits (or both). In either case, linkagedisequilibrium implies that the relevant loci are within sufficientphysical proximity along a length of a chromosome so that they segregatetogether with greater than random (i.e., non-random) frequency (in thecase of co-segregating traits, the loci that underlie the traits are insufficient proximity to each other). Markers that show linkagedisequilibrium are considered linked. Linked loci co-segregate more than50% of the time, e.g., from about 51% to about 100% of the time. Inother words, two markers that co-segregate have a recombinationfrequency of less than 50% (and, by definition, are separated by lessthan 50 cM on the same chromosome). As used herein, linkage can bebetween two markers, or alternatively between a marker and a phenotype.A marker locus can be “associated with” (linked to) a trait, e.g., P.sojae resistance. The degree of linkage of a genetic marker to aphenotypic trait is measured, e.g., as a statistical probability ofco-segregation of that genetic marker with the phenotype.

Linkage disequilibrium is most commonly assessed using the measure r²,which is calculated using the formula described by Hill and Robertson(Theor. Appl. Genet. 38:226 (1968)). When r²=1, complete linkagedisequilibrium exists between the two marker loci, meaning that themarkers have not been separated by recombination and have the sameallele frequency. Values for r² above ⅓ indicate sufficiently stronglinkage disequilibrium to be useful for mapping. Ardlie et al. (NatureReviews Genetics 3:299 (2002)). Hence, alleles are in linkagedisequilibrium when r² values between pairwise marker loci are greaterthan or equal to about 0.33, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1.0.

As used herein, the term “linkage equilibrium” describes a situationwhere two markers independently segregate, i.e., sort among progenyrandomly. Markers that show linkage equilibrium are considered unlinked(whether or not they lie on the same chromosome).

As used herein, the terms “marker” and “genetic marker” are usedinterchangeably to refer to a nucleotide and/or a nucleotide sequencethat has been associated with a phenotype and/or trait. A marker may be,but is not limited to, a SNP allele and/or combination of SNP alleles(haplotype) (Brookes, Gene 234:177 (1993)), a gene, a chromosomeinterval, a restriction fragment length polymorphism (RFLP), a simplesequence repeat (SSR), a random amplified polymorphic DNA (RAPD), acleaved amplified polymorphic sequence (CAPS) (Rafalski and Tingey,Trends in Genetics 9:275 (1993)), an amplified fragment lengthpolymorphism (AFLP) (Vos et al., Nucleic Acids Res. 23:4407 (1995)), asequence-characterized amplified region (SCAR) (Paran and Michelmore,Theor. Appl. Genet. 85:985 (1993)), a sequence-tagged site (STS)(Onozaki et al., Euphytica 138:255 (2004)), a single-strandedconformation polymorphism (SSCP) (Orita et al., Proc. Natl. Acad. Sci.USA 86:2766 (1989)), an inter-simple sequence repeat (ISSR) (Blair etal., Theor. Appl. Genet. 98:780 (1999)), an inter-retrotransposonamplified polymorphism (IRAP), a retrotransposon-microsatelliteamplified polymorphism (REMAP) (Kalendar et al., Theor. Appl. Genet.98:704 (1999)), an isozyme marker, an RNA cleavage product (such as aLynx tag) or any combination of the markers described herein. A markermay be present in genomic or expressed nucleic acids (e.g., ESTs). Alarge number of soybean genetic markers are known in the art, and arepublished or available from various sources, such as the SoyBaseinternet resource (www.soybase.org). In some embodiments, a geneticmarker of this invention is an SNP allele and/or combination of SNPalleles (haplotype), which are associated with Rps1 resistance.

Markers corresponding to genetic polymorphisms between members of apopulation can be detected by methods well-established in the art. Theseinclude, e.g., nucleic acid sequencing, hybridization methods,amplification methods (e.g., PCR-based sequence specific amplificationmethods), detection of restriction fragment length polymorphisms (RFLP),detection of isozyme markers, detection of polynucleotide polymorphismsby allele specific hybridization (ASH), detection of amplified variablesequences of the plant genome, detection of self-sustained sequencereplication, detection of simple sequence repeats (SSRs), detection ofsingle nucleotide polymorphisms (SNPs), and/or detection of amplifiedfragment length polymorphisms (AFLPs). Well established methods are alsoknown for detecting expressed sequence tags (ESTs) and SSR markersderived from EST sequences and randomly amplified polymorphic DNA(RAPD).

Accordingly, in some embodiments of this invention, a marker correspondsto an amplification product generated by amplifying a Glycine sp.nucleic acid with two oligonucleotide primers, for example, by thepolymerase chain reaction (PCR). As used herein, the phrase “correspondsto an amplification product” in the context of a marker refers to amarker that has a nucleotide sequence that is the same (allowing formutations introduced by the amplification reaction itself) as anamplification product that is generated by amplifying Glycine sp.genomic DNA with a particular set of primers. In some embodiments, theamplifying is by PCR, and the primers are PCR primers that are designedto hybridize to opposite strands of the Glycine sp. genomic DNA in orderto amplify a Glycine sp. genomic DNA sequence present between thesequences to which the PCR primers hybridize in the Glycine sp. genomicDNA. In other embodiments, a marker that “corresponds to” an amplifiedfragment is a marker that has the same sequence of one of the strands ofthe amplified fragment.

A “marker allele,” also described as an “allele of a marker locus,” canrefer to one of a plurality of polymorphic nucleotide sequences found ata marker locus in a population that is polymorphic for the marker locus.

“Marker-assisted selection” (MAS) is a process by which phenotypes areselected based on marker genotypes. Marker assisted selection includesthe use of marker genotypes for identifying plants for inclusion inand/or removal from a breeding program or planting.

As used herein, the terms “marker locus” and “marker loci” refer to aspecific chromosome location or locations in the genome of an organismwhere a specific marker or markers can be found. A marker locus can beused to track the presence of a second linked locus, e.g., a linkedlocus that encodes or contributes to expression of a phenotypic trait.For example, a marker locus can be used to monitor segregation ofalleles at a locus, such as a QTL or single gene, that are geneticallyor physically linked to the marker locus.

As used herein, the terms “marker probe” and “probe” refer to anucleotide sequence or nucleic acid molecule that can be used to detectthe presence of one or more particular alleles within a marker locus(e.g., a nucleic acid probe that is complementary to all of or a portionof the marker or marker locus, through nucleic acid hybridization).Marker probes comprising about 8, 10, 15, 20, 30, 40, 50, 60, 70, 80,90, 100 or more contiguous nucleotides may be used for nucleic acidhybridization. Alternatively, in some aspects, a marker probe refers toa probe of any type that is able to distinguish (i.e., genotype) theparticular allele that is present at a marker locus. Non-limitingexamples of probes of this invention include SEQ ID NOs:25-40.

As used herein, the term “molecular marker” may be used to refer to agenetic marker, as defined above, or an encoded product thereof (e.g., aprotein) used as a point of reference when identifying a linked locus. Amolecular marker can be derived from genomic nucleotide sequences orfrom expressed nucleotide sequences (e.g., from a spliced RNA, a cDNA,etc.). The term also refers to nucleotide sequences complementary to orflanking the marker sequences, such as nucleotide sequences used asprobes and/or primers capable of amplifying the marker sequence.Nucleotide sequences are “complementary” when they specificallyhybridize in solution, e.g., according to Watson-Crick base pairingrules. Some of markers can also be referred to as hybridization markerswhen located on an indel region. This is because the insertion regionis, by definition, a polymorphism vis-ã-vis a plant without theinsertion. Thus, the marker need only indicate whether the indel regionis present or absent. Any suitable marker detection technology may beused to identify such a hybridization marker.

As used herein, the term “primer” refers to an oligonucleotide which iscapable of annealing to a nucleic acid target and serving as a point ofinitiation of DNA synthesis when placed under conditions in whichsynthesis of a primer extension product is induced (e.g., in thepresence of nucleotides and an agent for polymerization such as DNApolymerase and at a suitable temperature and pH). A primer (in someembodiments an extension primer and in some embodiments an amplificationprimer) is in some embodiments single stranded for maximum efficiency inextension and/or amplification. In some embodiments, the primer is anoligodeoxyribonucleotide. A primer is typically sufficiently long toprime the synthesis of extension and/or amplification products in thepresence of the agent for polymerization. The minimum length of a primercan depend on many factors, including, but not limited to temperatureand composition (A/T vs. G/C content) of the primer.

In the context of amplification primers, these are typically provided asa pair of bi-directional primers consisting of one forward and onereverse primer or provided as a pair of forward primers as commonly usedin the art of DNA amplification such as in PCR amplification.

As such, it will be understood that the term “primer,” as used herein,can refer to more than one primer, particularly in the case where thereis some ambiguity in the information regarding the terminal sequence(s)of the target region to be amplified. Hence, a “primer” can include acollection of primer oligonucleotides containing sequences representingthe possible variations in the sequence or includes nucleotides whichallow a typical base pairing.

Primers can be prepared by any suitable method. Methods for preparingoligonucleotides of specific sequence are known in the art, and include,for example, cloning and restriction of appropriate sequences and directchemical synthesis. Chemical synthesis methods can include, for example,the phospho di- or tri-ester method, the diethylphosphoramidate methodand the solid support method disclosed in U.S. Pat. No. 4,458,066.

Primers can be labeled, if desired, by incorporating detectable moietiesby for instance spectroscopic, fluorescence, photochemical, biochemical,immunochemical, or chemical moieties.

The PCR method is well described in handbooks and known to the skilledperson. After amplification by PCR, target polynucleotides can bedetected by hybridization with a probe polynucleotide which forms astable hybrid with that of the target sequence under stringent tomoderately stringent hybridization and wash conditions. If it isexpected that the probes are essentially completely complementary (i.e.,about 99% or greater) to the target sequence, stringent conditions canbe used. If some mismatching is expected, for example if variant strainsare expected with the result that the probe will not be completelycomplementary, the stringency of hybridization can be reduced. In someembodiments, conditions are chosen to rule out non-specific/adventitiousbinding. Conditions that affect hybridization, and that select againstnon-specific binding are known in the art, and are described in, forexample, Sambrook & Russell (2001). Molecular Cloning: A LaboratoryManual, Third Edition, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y., United States of America. Generally, lower saltconcentration and higher temperature hybridization and/or washesincrease the stringency of hybridization conditions.

As used herein, the term “probe” refers to a single-strandedoligonucleotide sequence that will form a hydrogen-bonded duplex with acomplementary sequence in a target nucleic acid sequence analyte or itscDNA derivative.

Different nucleotide sequences or polypeptide sequences having homologyare referred to herein as “homologues.” The term homologue includeshomologous sequences from the same and other species and orthologoussequences from the same and other species. “Homology” refers to thelevel of similarity between two or more nucleotide sequences and/oramino acid sequences in terms of percent of positional identity (i.e.,sequence similarity or identity). Homology also refers to the concept ofsimilar functional properties among different nucleic acids, aminoacids, and/or proteins.

As used herein, the phrase “nucleotide sequence homology” refers to thepresence of homology between two polynucleotides. Polynucleotides have“homologous” sequences if the sequence of nucleotides in the twosequences is the same when aligned for maximum correspondence. The“percentage of sequence homology” for polynucleotides, such as 50, 55,60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or 100 percent sequencehomology, can be determined by comparing two optimally aligned sequencesover a comparison window (e.g., about 20-200 contiguous nucleotides),wherein the portion of the polynucleotide sequence in the comparisonwindow can include additions or deletions (i.e., gaps) as compared to areference sequence for optimal alignment of the two sequences. Optimalalignment of sequences for comparison can be conducted by computerizedimplementations of known algorithms, or by visual inspection. Readilyavailable sequence comparison and multiple sequence alignment algorithmsare, respectively, the Basic Local Alignment Search Tool (BLAST;Altschul et al. (1990) J Mol Biol 215:403-10; Altschul et al. (1997)Nucleic Acids Res 25:3389-3402) and ClustalX (Chenna et al. (2003)Nucleic Acids Res 31:3497-3500) programs, both available on theInternet. Other suitable programs include, but are not limited to, GAP,BestFit, PlotSimilarity, and FASTA, which are part of the Accelrys GCGPackage available from Accelrys Software, Inc. of San Diego, Calif.,United States of America.

As used herein “sequence identity” refers to the extent to which twooptimally aligned polynucleotide or polypeptide sequences are invariantthroughout a window of alignment of components, e.g., nucleotides oramino acids. “Identity” can be readily calculated by known methodsincluding, but not limited to, those described in: ComputationalMolecular Biology (Lesk, A. M., ed.) Oxford University Press, New York(1988); Biocomputing: Informatics and Genome Projects (Smith, D. W.,ed.) Academic Press, New York (1993); Computer Analysis of SequenceData, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press,New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje,G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov,M. and Devereux, J., eds.) Stockton Press, New York (1991).

As used herein, the term “substantially identical” or “corresponding to”means that two nucleotide sequences have at least 50%, 60%, 70%, 75%,80%, 85%, 90% or 95% sequence identity. In some embodiments, the twonucleotide sequences can have at least 85%, 90%, 95%, 96%, 97%, 98%, 99%or 100% sequence identity.

An “identity fraction” for aligned segments of a test sequence and areference sequence is the number of identical components which areshared by the two aligned sequences divided by the total number ofcomponents in the reference sequence segment, i.e., the entire referencesequence or a smaller defined part of the reference sequence. Percentsequence identity is represented as the identity fraction multiplied by100. As used herein, the term “percent sequence identity” or “percentidentity” refers to the percentage of identical nucleotides in a linearpolynucleotide sequence of a reference (“query”) polynucleotide molecule(or its complementary strand) as compared to a test (“subject”)polynucleotide molecule (or its complementary strand) when the twosequences are optimally aligned (with appropriate nucleotide insertions,deletions, or gaps totaling less than 20 percent of the referencesequence over the window of comparison). In some embodiments, “percentidentity” can refer to the percentage of identical amino acids in anamino acid sequence.

Optimal alignment of sequences for aligning a comparison window is wellknown to those skilled in the art and may be conducted by tools such asthe local homology algorithm of Smith and Waterman, the homologyalignment algorithm of Needleman and Wunsch, the search for similaritymethod of Pearson and Lipman, and optionally by computerizedimplementations of these algorithms such as GAP, BESTFIT, FASTA, andTFASTA available as part of the GCG® Wisconsin Package® (Accelrys Inc.,Burlington, Mass.). The comparison of one or more polynucleotidesequences may be to a full-length polynucleotide sequence or a portionthereof, or to a longer polynucleotide sequence. For purposes of thisinvention “percent identity” may also be determined using BLASTX version2.0 for translated nucleotide sequences and BLASTN version 2.0 forpolynucleotide sequences.

The percent of sequence identity can be determined using the “Best Fit”or “Gap” program of the Sequence Analysis Software Package™ (Version 10;Genetics Computer Group, Inc., Madison, Wis.). “Gap” utilizes thealgorithm of Needleman and Wunsch (Needleman and Wunsch, J Mol. Biol.48:443-453, 1970) to find the alignment of two sequences that maximizesthe number of matches and minimizes the number of gaps. “BestFit”performs an optimal alignment of the best segment of similarity betweentwo sequences and inserts gaps to maximize the number of matches usingthe local homology algorithm of Smith and Waterman (Smith and Waterman,Adv. Appl. Math., 2:482-489, 1981, Smith et al., Nucleic Acids Res.11:2205-2220, 1983).

Useful methods for determining sequence identity are also disclosed inGuide to Huge Computers (Martin J. Bishop, ed., Academic Press, SanDiego (1994)), and Carillo et al. (Applied Math 48:1073(1988)). Moreparticularly, preferred computer programs for determining sequenceidentity include but are not limited to the Basic Local Alignment SearchTool (BLAST) programs which are publicly available from National CenterBiotechnology Information (NCBI) at the National Library of Medicine,National Institute of Health, Bethesda, Md. 20894; see BLAST Manual,Altschul et al., NCBI, NLM, NIH; (Altschul et al., J. Mol. Biol.215:403-410 (1990)); version 2.0 or higher of BLAST programs allows theintroduction of gaps (deletions and insertions) into alignments; forpeptide sequence BLASTX can be used to determine sequence identity; andfor polynucleotide sequence BLASTN can be used to determine sequenceidentity.

As used herein, the terms “phenotype,” “phenotypic trait” or “trait”refer to one or more traits of an organism. The phenotype can beobservable to the naked eye, or by any other means of evaluation knownin the art, e.g., microscopy, biochemical analysis, or anelectromechanical assay. In some cases, a phenotype is directlycontrolled by a single gene or genetic locus, i.e., a “single genetrait.” In other cases, a phenotype is the result of several genes.

As used herein, the term “polymorphism” refers to a variation in thenucleotide sequence at a locus, where the variation is too common to bedue merely to a spontaneous mutation. A polymorphism must have afrequency of at least about 1% in a population. A polymorphism can be asingle nucleotide polymorphism (SNP), or an insertion/deletionpolymorphism, also referred to herein as an “indel.” Additionally, thevariation can be in a transcriptional profile or a methylation pattern.The polymorphic site or sites of a nucleotide sequence can be determinedby comparing the nucleotide sequences at one or more loci in two or moregermplasm entries.

As used herein, the term “plant” can refer to a whole plant, any partthereof, or a cell or tissue culture derived from a plant. Thus, theterm “plant” can refer to a whole plant, a plant component or a plantorgan (e.g., leaves, stems, roots, etc.), a plant tissue, a seeds and/ora plant cell. A plant cell is a cell of a plant, taken from a plant, orderived through culture from a cell taken from a plant.

As used herein, the term “plant part” includes but is not limited toembryos, pollen, seeds, leaves, flowers (including but not limited toanthers, ovules and the like), fruit, stems or branches, roots, roottips, cells including cells that are intact in plants and/or parts ofplants, protoplasts, plant cell tissue cultures, plant calli, plantclumps, and the like. Thus, a plant part includes soybean tissuecultures from which soybean plants can be regenerated. Further, as usedherein, “plant cell” refers to a structural and physiological unit ofthe plant, which comprises a cell wall and also may refer to aprotoplast. A plant cell of the present invention can be in the form ofan isolated single cell or can be a cultured cell or can be a part of ahigher-organized unit such as, for example, a plant tissue or a plantorgan.

As used herein, the term “soybean” refers to a plant, and any partthereof, of the genus Glycine including, but not limited to, Glycinemax.

As used herein, the term “population” refers to a geneticallyheterogeneous collection of plants sharing a common genetic derivation.

As used herein, the terms “progeny,” “progeny plant,” and/or “offspring”refer to a plant generated from a vegetative or sexual reproduction fromone or more parent plants. A progeny plant may be obtained by cloning orselfing a single parent plant, or by crossing two parental plants andincludes selfings as well as the F1 or F2 or still further generations.An F1 is a first-generation offspring produced from parents at least oneof which is used for the first time as donor of a trait, while offspringof second generation (F2) or subsequent generations (F3, F4, and thelike) are specimens produced from selfings or crossings of F1s, F2s andthe like. Thus, an F1 can be a hybrid resulting from a cross between twotrue breeding parents (the phrase “true-breeding” refers to anindividual that is homozygous for one or more traits), while an F2 canbe an offspring resulting from self-pollination of the F1 hybrids.

As used herein, the term “reference sequence” refers to a definednucleotide sequence used as a basis for nucleotide sequence comparison(e.g., Chromosome 3 of Glycine max cultivar Williams 82). The referencesequence for a marker, for example, can be obtained by genotyping anumber of lines at the locus or loci of interest, aligning thenucleotide sequences in a sequence alignment program, and then obtainingthe consensus sequence of the alignment. Hence, a reference sequenceidentifies the polymorphisms in alleles at a locus. A reference sequencemay not be a copy of an actual nucleic acid sequence from any particularorganism; however, it is useful for designing primers and probes foractual polymorphisms in a locus or loci.

Genetic Mapping

Genetic loci correlating with particular phenotypes, such as resistanceto P. sojae, can be mapped in an organism's genome. By identifying amarker or cluster of markers that co-segregate with a trait of interest,the breeder is able to rapidly select a desired phenotype by selectingfor the proper marker (a process called marker-assisted selection, orMAS). Such markers may also be used by breeders to design genotypes insilico and to practice whole genome selection.

The present invention provides markers associated with Rps1 resistancealleles and thus, associated with resistance to particular races of P.sojae. Detection of these markers and/or other linked markers can beused to identify, select and/or produce plants having Rps1 resistancealleles, and thus, having resistance to P. sojae and/or to eliminateplants from breeding programs or from planting that do not have a Rps1resistance allele and are not resistant to P. sojae.

Markers Associated with an Rps1 Resistance Allele

Molecular markers are used for the visualization of differences innucleic acid sequences. This visualization can be due to DNA-DNAhybridization techniques after digestion with a restriction enzyme(e.g., an RFLP) and/or due to techniques using the polymerase chainreaction (e.g., SNP, STS, SSR/microsatellites, AFLP, and the like). Insome embodiments, all differences between two parental genotypessegregate in a mapping population based on the cross of these parentalgenotypes. The segregation of the different markers can be compared andrecombination frequencies can be calculated. Methods for mapping markersin plants are disclosed in, for example, Glick & Thompson (1993) Methodsin Plant Molecular Biology and Biotechnology, CRC Press, Boca Raton,Fla., United States of America; Zietkiewicz et al. (1994) Genomics20:176-183.

The recombination frequencies of genetic markers on differentchromosomes and/or in different linkage groups are generally 50%.Between genetic markers located on the same chromosome or in the samelinkage group, the recombination frequency generally depends on thephysical distance between the markers on a chromosome. A lowrecombination frequency typically corresponds to a low genetic distancebetween markers on a chromosome. Comparison of all recombinationfrequencies among a set of genetic markers results in the most logicalorder of the genetic markers on the chromosomes or in the linkagegroups. This most logical order can be depicted in a linkage map. Agroup of adjacent or contiguous markers on the linkage map that isassociated with an increased level of resistance to a disease (e.g., toa reduced incidence of acquiring the disease upon infectious contactwith the disease agent and/or a reduced lesion growth rate uponestablishment of infection) can provide the position of a locusassociated with resistance to that disease. The present inventionprovides SNP markers and/or combination of SNP markers that can be usedin various aspects of the presently disclosed subject matter as setforth herein.

Thus, the SNP markers provided herein can be used for detecting thepresence of one or more Rps1 resistance alleles in soybean plant orgermplasm, and can therefore be used in methods involvingmarker-assisted breeding and selection of P. sojae-resistant soybeanplants/soybean plants having one or more Rps1 resistance alleles.

In some embodiments, methods for detecting the presence of an SNP in asoybean plant or germplasm can comprise providing a oligonucleotide orpolynucleotide capable of hybridizing under stringent hybridizationconditions to a nucleotide sequence of a SNP disclosed herein,contacting the oligonucleotide or polynucleotide with genomic nucleicacid (or a fragment thereof, including, but not limited to a restrictionfragment thereof) of the soybean plant or germplasm, and determining thepresence of the SNP by the specific hybridization of the oligonucleotideor polynucleotide to the soybean genomic nucleic acid (or the fragmentthereof).

Accordingly, SNP markers associated with Rps1 resistance alleles areidentified herein. The SNP markers of the present invention aredescribed herein with respect to their position in Chromosome 3 (linkagegroup N) of the soybean genome (e.g., Glycine max L. cultivar Williams82) (reference sequence found at the Soybase database, www.soybase.org).Thus, Table 1 provides each of the markers of this invention with theircorresponding name, sequence identifier (SEQ ID NO), the location of theSNP on Chromosome 3 of soybean cultivar Williams 82 (8X public build;SoyBase internet resource (www.soybase.org/SequenceIntro.php)), thetarget resistance allele and non-target allele at that location, thegene that is tagged by the marker and associated amplification primersand marker probes.

TABLE 1 Description of the SNP markers and related data. Marker AllelesMarker Sequence (SEQ ID NO) Position in Amplification Reference(location of Reference Associated Primer Pair Marker Probes SequenceName allele) Sequence Allele 1 Allele 2 Gene (SEQ ID NO) (SEQ ID NO)Glycine SY2723AQ 1 (nt 251) 3,832,550 T A Rps1-a  9, 10 25/26 max L.SY2721AQ 2 (nt 251) 3,634,150 C A Rps1-a, 11, 12 27/28 cultivar Rps1-cWilliams SY2724AQ 3 (nt 251) 4,474,011 C G Rps1-c 13, 14 29/30 82SY2726BQ 4 (nt 251) 4,632,793 G C Rps1-c 15, 16 31/32 (Gm03) SY2726DQ 5(nt 251) 4,633,039 A C Rps1-c 17, 18 33/34 SY2724BQ 6 (nt 251) 4,474,754A G Rps1c, 19, 20 35/36 Rps1-k SY2724CQ 7 (nt 251) 4,474,791 A G Rps1c,21, 22 37/38 Rps1-k SY2725AQ 8 (nt 251) 4,531,558 A G Rps1-k 23, 2439/40

As shown in Table 1, the SNP markers of this invention are associatedwith the Rps1 resistance alleles, Rps1-a, Rps1-c, and Rps1-k. In someembodiments of this invention, the SNP marker can be associated withmore than one Rps1 allele. In some embodiments, as described herein, acombination of SNPs can be used to detect the presence of an Rps1resistance allele.

In further embodiments, a marker of this invention can include anymarker linked to the aforementioned markers. Linked markers may bedetermined, for example, by using resources available on the SoyBaseinternet resource (www.soybase.org).

The presently disclosed subject matter thus also relates to methods foridentifying, selecting, and/or producing soybean plants having an Rps1resistance allele comprising detecting in a donor soybean plant thepresence of a genetic marker associated with an Rps1 resistance alleleand/or a genetic marker associated with P. sojae resistance as describedherein and transferring the nucleotide sequence comprising the at leastone genetic marker thus detected from the donor soybean plant to a P.sojae-recipient soybean plant. It is noted that the recipient soybeanplant can be resistant to certain P. sojae races and susceptible toother P. sojae races. Typically, the recipient soybean plant is at leastsusceptible to the race of P. sojae for which the transfer of thenucleotide sequence comprising the genetic marker (associated with anRps1 resistance allele) confers resistance (transferred from the donorsoybean plant). In other embodiments, the recipient soybean plant cansusceptible to all P. sojae races. This allows the breeder to developsoybean plants having resistance to one or more races of P. sojae. Thetransfer of the nucleotide sequence can be performed by any of themethods described herein.

Thus, methods for identifying, selecting and/or producing a soybeanplant or germplasm comprising an Rps1 resistance allele can comprisedetecting the presence of a genetic marker associated with an Rps1resistance allele. The SNP marker can be detected in any sample takenfrom the soybean plant or germplasm, including, but not limited to, thewhole plant or germplasm, a portion of said plant or germplasm (e.g., acell, leaf, seed, etc, from said plant or germplasm) or a nucleotidesequence from said plant or germplasm.

Accordingly, in one aspect of the present invention, a method ofidentifying and/or selecting a soybean plant or germplasm having an Rps1resistance allele is provided, the method comprising: detecting, in asoybean plant or germplasm, the presence of a genetic marker associatedwith an Rps1 resistance allele, wherein said marker comprises, consistsessentially of, or consists of (1) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ); (2) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ); (3) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ);(4) an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (5) an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (6) an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (7) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (8) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:2(SY2721AQ); (9) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (10) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ); (11) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), and a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (12) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), and a G alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (13) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ) and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(14) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (15) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(16) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (17) wherein the SNPis an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (18) is a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (19) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (20) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(21) an A allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (22) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (23) an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (24) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (25) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (26) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (27) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (28) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (29) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (30) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (31) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (32) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ), (33) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (34) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (36) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(37) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(39) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(41) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (46) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above, thereby identifying and/orselecting a soybean plant or germplasm having an Rps1 resistance allele.

In a further aspect, a method is provided for identifying and/orselecting a P. sojae-resistant soybean plant or germplasm, the methodcomprising: detecting, in a soybean plant or germplasm, the presence ofa genetic marker associated with an Rps1 allele conferring resistance toP. sojae, wherein the genetic marker comprises, consists essentially of,or consists of (1) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ); (2) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(3) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ); (4) an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (5) an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (6) an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (7) an A allele at nucleotide 251 of SEQID NO:8 (SY2725AQ); (8) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:2 (SY2721AQ);(9) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a Gallele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (10) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ); (11) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), and a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(12) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), and a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (13) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (14) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (15) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(16) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (17) wherein the SNPis an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (18) is a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (19) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (20) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(21) an A allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (22) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (23) an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (24) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (25) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (26) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (27) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (28) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (29) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (30) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (31) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (32) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ), (33) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (34) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (36) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(37) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(39) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(41) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (46) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above, thereby identifying and/orselecting a P. sojae-resistant soybean plant or germplasm.

Methods for identifying and/or selecting a soybean plant or germplasmcomprising an Rps1 resistance allele and methods for identifying and/orselecting a P. sojae-resistant soybean plant or germplasm can comprisedetecting the presence of a marker or a combination of markersassociated with an Rps1 resistance allele as described herein (i.e.,Rps1-a, Rps1-c, Rps1-k, or any combination thereof).

Thus, in some embodiments, the present invention provides methods ofidentifying and/or selecting a soybean plant or germplasm having anRps1-a resistance allele and/or a P. sojae-resistant soybean plant orgermplasm, the methods comprising: detecting, in a soybean plant orgermplasm, the presence of a genetic marker associated with an Rps1-aresistance allele, wherein said genetic marker comprises: (1) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ); (2) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele at nucleotide251 of SEQ ID NO:2 (SY2721AQ); (3) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ) and a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ); (4) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (5) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), and a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (6) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), and a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(7) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (8) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ), or any combination thereof,thereby identifying and/or selecting a soybean plant or germplasm and/ora P. sojae-resistant soybean plant or germplasm having an Rps1-aresistance allele.

In other embodiments, the present invention provides a method ofidentifying and/or selecting a soybean plant or germplasm having anRps1-c resistance allele and/or a Phytophthora sojae-resistant soybeanplant or germplasm, the method comprising: detecting, in a soybean plantor germplasm, the presence of a genetic marker associated with an Rps1-cresistance allele, wherein said marker comprises: (1) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ); (2) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ); (3) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ); (4) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(5) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (6) wherein the SNPis an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (7) is a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (8) a G allele at nucleotide 251 of SEQID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQ ID NO:6(SY2724BQ); (9) an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ)and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (10) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (11) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); or any combination thereof,thereby identifying and/or selecting a soybean plant or germplasm and/ora P. sojae-resistant soybean plant or germplasm having an Rps1-cresistance allele.

In further embodiments, the present invention provides a method ofidentifying and/or selecting a soybean plant or germplasm and/or a P.sojae-resistant soybean plant or germplasm having an Rps1-k resistanceallele is provided, the method comprising: detecting, in a soybean plantor germplasm, the presence of a genetic marker associated with an Rps1-kresistance allele, wherein said genetic marker comprises: (1) an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (2) an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (3) an A allele at nucleotide 251 of SEQID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:6(SY2724BQ); (4) a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (5) a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (6) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (7) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (8) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (9) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (10) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (11) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ), (12) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (13) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), (14) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); or any combination thereof, thereby of identifyingand/or selecting a soybean plant or germplasm and/or a P.sojae-resistant soybean plant or germplasm having an Rps1-k resistanceallele.

In additional embodiments, the present invention provides a method ofidentifying and/or selecting a soybean plant or germplasm and/or a P.sojae-resistant soybean plant or germplasm having an Rps1-a resistanceallele and an Rps1-c resistance allele, the method comprising:detecting, in a soybean plant or germplasm, the presence of a geneticmarker associated with an Rps1-a and an Rps1c resistance allele, whereinsaid genetic marker comprises: (1) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ); (2) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (3) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (4) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); or any combination thereof,thereby identifying and/or selecting a soybean plant or germplasm and/ora P. sojae-resistant soybean plant or germplasm having an Rps1-aresistance allele and an Rps1-c resistance allele.

In some embodiments, the present invention provides a method ofidentifying and/or selecting a soybean plant or germplasm and/or a P.sojae-resistant soybean plant or germplasm having an Rps1-a resistanceallele and an Rps1-k resistance allele, the method comprising:detecting, in a soybean plant or germplasm, the presence of a geneticmarker associated with an Rps1-a and an Rps1k resistance allele, whereinsaid genetic marker comprises: (1) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (2) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (3) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ); (4) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (5) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (6) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (7) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (11) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination thereof, thereby identifying and/or selecting asoybean plant or germplasm and/or a P. sojae-resistant soybean plant orgermplasm having an Rps1-a resistance allele and an Rps1-k resistanceallele.

In some embodiments, the present invention provides a method ofidentifying and/or selecting a soybean plant or germplasm and/or a P.sojae-resistant soybean plant or germplasm having an Rps1-c resistanceallele and an Rps1-k resistance allele, the method comprising:detecting, in a soybean plant or germplasm, the presence of a geneticmarker associated with an Rps1-c and an Rps1k resistance allele, whereinsaid genetic marker comprises: (1) an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (2) an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (3) C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ) andan A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (4) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (5) a C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (6) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (7) an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ; (8) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (9) an A alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (10) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); or any combination thereof,thereby identifying and/or selecting a soybean plant or germplasm and/ora P. sojae-resistant soybean plant or germplasm having an Rps1-cresistance allele and an Rps1-k resistance allele.

In other embodiments, the present invention provides a method ofidentifying and/or selecting a soybean plant or germplasm and/or a P.sojae-resistant soybean plant or germplasm having an Rps1-a resistanceallele, an Rps1-c resistance allele and an Rps1-k resistance allele, themethod comprising: detecting, in a soybean plant or germplasm, thepresence of a genetic marker associated with an Rps1-a, Rps1-c, and anRps1k resistance allele, wherein said genetic marker comprises, consistsessentially of, or consists of: (1) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),(2) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (3) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), is a C allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (4) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (5) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); or any combination thereof,thereby identifying and/or selecting a soybean plant or germplasm and/ora P. sojae-resistant soybean plant or germplasm having an Rps1-aresistance allele, an Rps1-c resistance allele and an Rps1-k resistanceallele.

In other aspects, the present invention provides a method of identifyingand/or selecting a P. sojae-susceptible soybean plant or germplasm, themethod comprising: detecting, in said soybean plant or germplasm, thepresence of a genetic marker associated with an Rps1 susceptible allele,wherein said genetic marker comprises, consists essentially of, orconsists of: (1) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ); (2) an A allele at nucleotide 251 of SEQ ID NO:2 (SY2721AQ);(3) a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (4) a Callele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ); (5) a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ); (6) an G allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (7) an G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (8) a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (9) an A allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ); (10) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and aG allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (11) an A alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ) and a G allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ); (12) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), is a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ)and a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); or anycombination thereof, thereby identifying and/or selecting a P.sojae-susceptible soybean plant or germplasm. Thus, for example, byidentifying plants having these particular genetic markers these plantscan be removed from the breeding population.

Exemplary Assay Primers for Genotyping and/or Amplification

As discussed herein, in some embodiments of this invention, a marker canbe identified using amplification products generated by amplifying aGlycine sp. nucleic acid with two oligonucleotide primers. In someembodiments, the amplification is by PCR, and the primers are PCRprimers that are designed to hybridize to opposite strands of theGlycine sp. genomic DNA (e.g., Chromosome 3) in order to amplify aGlycine sp. genomic DNA sequence present between the sequences to whichthe PCR primers hybridize in the Glycine sp. genomic DNA. Methods ofamplifying nucleic acids are well known in the art.

Accordingly, in some embodiments of the present invention, a method ofidentifying and/or selecting a soybean plant or germplasm having an Rps1resistance allele is provided, the method comprising: detecting, in saidsoybean plant or germplasm, the presence of a genetic marker associatedwith the Rps1 resistance allele, wherein said marker is detected inamplification products from a nucleic acid sample isolated from saidsoybean plant or germplasm using a probe, said amplification productshaving been produced using pairs of amplification primers wherein saidamplification primers and probes have the nucleotide sequences of: (a)SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:25 and SEQ ID NO:26, respectivelyfor SY2723AQ; (b) SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:27 and SEQ IDNO:28, respectively for SY2721AQ; (c) SEQ ID NO:13, SEQ ID NO:14, SEQ IDNO:29 and SEQ ID NO:30, respectively for SY2724AQ; (d) SEQ ID NO:15, SEQID NO:16, SEQ ID NO:31 and SEQ ID NO:32, respectively for SY2726BQ; (e)SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:33 and SEQ ID NO:34, respectivelyfor SY2726DQ; (f) SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:35 and SEQ IDNO:36, respectively for SY2724BQ; (g) SEQ ID NO:21, SEQ ID NO:22, SEQ IDNO:37, and SEQ ID NO:38, respectively for SY2724CQ; (h) SEQ ID NO:23 andSEQ ID NO:24, SEQ ID NO:39, and SEQ ID NO:40, respectively for SY2725AQ,(i) or any combination of (a) through (h) above, thereby identifyingand/or selecting a soybean plant or germplasm having an Rps1 resistanceallele.

In other embodiments, a method of producing a soybean plant or germplasmhaving an Rps1 resistance allele is provided, the method comprising: (a)detecting, in said soybean plant or germplasm, the presence of a geneticmarker associated with the Rps1 resistance allele, wherein said markeris detected in amplification products from a nucleic acid sampleisolated from said soybean plant or germplasm using a probe, saidamplification products having been produced using pairs of amplificationprimers, wherein said amplification primers and probes have thenucleotide sequences of: (a) SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:25 andSEQ ID NO:26, respectively for SY2723AQ; (b) SEQ ID NO:11, SEQ ID NO:12,SEQ ID NO:27 and SEQ ID NO:28, respectively for SY2721AQ; (c) SEQ IDNO:13, SEQ ID NO:14, SEQ ID NO:29 and SEQ ID NO:30, respectively forSY2724AQ; (d) SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:32,respectively for SY2726BQ; (e) SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:33and SEQ ID NO:34, respectively for SY2726DQ; (f) SEQ ID NO:19, SEQ IDNO:20, SEQ ID NO:35 and SEQ ID NO:36, respectively for SY2724BQ; (g) SEQID NO:21, SEQ ID NO:22, SEQ ID NO:37, and SEQ ID NO:38, respectively forSY2724CQ; (h) SEQ ID NO:23 and SEQ ID NO:24, SEQ ID NO:39, and SEQ IDNO:40, respectively for SY2725AQ, (i) or any combination of (a) through(h) above; and (b) producing a soybean plant from said soybeangermplasm, thereby producing a soybean plant or germplasm having an Rps1resistance allele. As the skilled artisan would readily recognize, whencombinations of SNPs are detected, then combinations of primers andprobes are used.

Marker-Assisted Selection

The subject matter disclosed herein also relates to methods forproducing pathogen-resistant soybean plants comprising detecting thepresence of a genetic marker associated with pathogen resistance in adonor soybean plant according to the methods as described herein andtransferring a nucleic acid sequence comprising at least one geneticmarker thus detected from the donor plant to a recipient soybean plant.The transfer of the nucleic acid sequence can be performed by any methodknown in the art.

Thus, the present invention encompasses methods of plant breeding andmethods of selecting/identifying plants, in particular soybean plants,particularly cultivated soybean plants as breeder plants for use inbreeding programs or cultivated soybean plants having desired genotypicor potential phenotypic properties, in particular related to producingvaluable soybeans, also referred to herein as commercially valuableplants. Herein, a cultivated plant is defined as a plant being purposelyselected or having been derived from a plant having been purposelyselected in agricultural or horticultural practice for having desiredgenotypic or potential phenotypic properties, for example a plantobtained by inbreeding.

The presently disclosed subject matter thus also provides methods forselecting a plant of the genus Glycine having P. sojae resistancecomprising detecting in the plant the presence of one or more Rps1resistance alleles as defined herein. In an exemplary embodiment of thepresently disclosed methods for selecting such a plant, the methodcomprises providing a sample of genomic DNA from a soybean plant; and(b) detecting in the sample of genomic DNA at least one genetic markerassociated with P. sojae resistance. In some embodiments, the detectingcomprises detecting one or more SNPs that are associated with P. sojaeresistance.

The providing of a sample of genomic DNA from a soybean plant can beperformed by standard DNA isolation methods well known in the art.

The detecting of a genetic marker (e.g., SNP, combination of SNPs) canin some embodiments comprise the use of one or more sets of primer pairs(SNP assays) that can be used to produce one or more amplificationproducts that can be used in the detection of genetic markers (SNPs).Such a set of primers can comprise, in some embodiments, nucleotidesequences as set forth in SEQ ID NOs:9-24.

In some embodiments, the detecting of a genetic marker can comprise theuse of a nucleic acid probe having a nucleotide base sequence that issubstantially complementary to the nucleic acid sequence defining thegenetic marker and which nucleic acid probe specifically hybridizesunder stringent conditions with a nucleic acid sequence defining thegenetic marker. A suitable nucleic acid probe can for instance be asingle strand of the amplification product corresponding to the marker.In some embodiments, the detecting of a genetic marker is designed todetermine whether a particular allele of a SNP is present or absent in aparticular plant.

The presently disclosed subject matter thus also relates to methods forproducing pathogen-resistant soybean plants comprising detecting thepresence of a genetic marker associated with an Rps1 resistance allele(or a genetic marker associated with P. sojae resistance) in a donorsoybean plant according to the presently disclosed subject matter asdescribed herein and transferring a nucleotide sequence comprising atleast one genetic marker thus detected, or a P. sojaeresistance-conferring part thereof, from the donor plant to a recipientsoybean plant. In particular embodiments, the recipient soybean plant issusceptible to the race of P. sojae for which said transferrednucleotide sequence confers resistance. The transfer of the nucleic acidsequence can be performed by any of the methods described herein.

An exemplary embodiment of such a method comprises the transfer of thenucleic acid sequence from a pathogen-resistant donor soybean plant intoa recipient soybean plant by crossing the plants by introgression. Thistransfer can be accomplished by using traditional breeding techniques.Pathogen-resistance loci are introgressed in some embodiments intocommercial soybean varieties using marker-assisted selection (MAS) ormarker-assisted breeding (MAB). MAS and MAB involves the use of one ormore of the molecular markers, identified as having a significantlikelihood of co-segregation with a desired trait, and used for theidentification and selection of those offspring plants that contain oneor more of the genes that encode for the desired trait. As disclosedherein, such identification and selection is based on selection of SNPalleles of this invention or markers associated therewith. MAB can alsobe used to develop near-isogenic lines (NIL) comprising one or morepathogen resistant alleles of interest, allowing a more detailed studyof an effect of such allele(s). MAB is also an effective method fordevelopment of backcross inbred line (BIL) populations. Soybean plantsdeveloped according to these embodiments can in some embodiments derivea majority of their traits from the recipient plant, and derive pathogenresistance from the donor plant. MAB/MAS techniques increase theefficiency of backcrossing and introgressing genes using marker-assistedselection (MAS) or marker-assisted breeding (MAB).

Thus, traditional breeding techniques can be used to introgress anucleic acid sequence associated with pathogen resistance into arecipient soybean plant. The recipient soybean plant may be resistant orsusceptible to one or more pathogens or to one or more P. sojae races.In some embodiments of the present invention, the recipient soybeanplant is susceptible to the P. sojae race for which resistance isconferred by trnaferring said nucleic acid sequence associated withpathogen resistance. Thus, for example, inbred pathogen-resistantsoybean plant lines can be developed using the techniques of recurrentselection and backcrossing, selfing, and/or dihaploids, or any othertechnique used to make parental lines. In a method of recurrentselection and backcrossing, pathogen resistance can be introgressed intoa target recipient plant (the recurrent parent) by crossing therecurrent parent with a first donor plant, which differs from therecurrent parent (i.e., non-recurrent parent). The recurrent parent is aplant that is non-resistant or has a low level of resistance to one ormore pathogens or to a particular race of a pathogen but, in someembodiments, possesses commercially desirable characteristics, such as,but not limited to (additional) disease and/or insect resistance,valuable nutritional characteristics, valuable abiotic stress tolerance(including, but not limited to, drought tolerance, salt tolerance), andthe like. In some embodiments, the non-recurrent parent exhibitspathogen resistance and comprises a nucleic acid sequence that isassociated with pathogen resistance (e.g., resistance to P. sojae). Thenon-recurrent parent can be any plant variety or inbred line that iscross-fertile with the recurrent parent.

In some embodiments, the progeny resulting from a cross between therecurrent parent and non-recurrent parent are backcrossed to therecurrent parent. The resulting plant population is then screened forthe desired characteristics, which screening can occur in a number ofdifferent ways. For instance, the population can be screened usingphenotypic pathology screens or quantitative bioassays as known in theart. Alternatively, instead of using bioassays, MAB can be performedusing one or more of the hereinbefore described molecular markers,hybridization probes, or polynucleotides to identify those progeny thatcomprise a nucleic acid sequence encoding, for example, P. sojaeresistance or a genetic marker associated with P. sojae resistance(e.g., SNPs and SNP combinations described herein). Also, MAB can beused to confirm the results obtained from the quantitative bioassays. Insome embodiments, the markers defined herein are suitable to selectproper offspring plants by genotypic screening.

Following screening, F1 hybrid plants that exhibit a pathogen-resistantphenotype or, in some embodiments, the genotype, and thus comprise therequisite nucleic acid sequence associated with pathogen resistance, arethen selected and backcrossed to the recurrent parent in order to allowfor the soybean plant to become increasingly inbred. The process ofselecting and backcrossing can be repeated for a number of generations(e.g., for one, two, three, four, five, six, seven, eight, or moregenerations).

Thus, a marker that demonstrates linkage with a locus affecting adesired phenotypic trait provides a useful tool for selection of thetrait in a plant population. This is particularly true where thephenotype is difficult to assay or occurs at a late stage in plantdevelopment. Since marker assays are less laborious and take up lessphysical space than field phenotyping, much larger populations can beassayed, increasing the chances of finding a recombinant plant with thetarget segment from the donor line that is moved to the recipient line.The closer the linkage, the more useful the marker, as recombination isless likely to occur between the marker and the gene that causes orimparts the trait. In addition, having flanking markers can decrease thechance that false positive selection will occur. Ideally, a marker is inthe gene itself, so that recombination cannot occur between the markerand the gene. Such a marker is called a “perfect marker.”

The availability of integrated linkage maps of the soybean genomecontaining increasing densities of public soybean markers hasfacilitated soybean genetic mapping and MAS. See, e.g.soybeanbreederstoolbox.org, which can be found on the SoyBase internetresource (www.soybase.org).

Of the types genetic marker available, SNPs are some of the mostabundant and have the potential to provide the highest genetic mapresolution (Bhattramakki et al., Plant Molec. Biol. 48:539 (2002)). SNPscan be assayed in a so-called “ultra-high-throughput” fashion becausethey do not require large amounts of nucleic acid and automation of theassay is straight-forward. SNPs also have the benefit of beingrelatively low-cost systems. These three factors together make SNPshighly attractive for use in MAS. Several methods are available for SNPgenotyping, including but not limited to, hybridization, primerextension, oligonucleotide ligation, nuclease cleavage, minisequencingand coded spheres. Such methods have been reviewed in variouspublications: Gut, Hum. Mutat. 17:475 (2001); Shi, Clin. Chem. 47:164(2001); Kwok, Pharmacogenomics 1:95 (2000); Bhattramakki and Rafalski,Discovery and application of single nucleotide polymorphism markers inplants, in PLANT GENOTYPING: THE DNA FINGERPRINTING OF PLANTS, CABIPublishing, Wallingford (2001). A wide range of commercially availabletechnologies utilize these and other methods to interrogate SNPs,including Masscode™ (Qiagen, Germantown, Md.), Invader® (Hologic,Madison, Wis.), SnapShot® (Applied Biosystems, Foster City, Calif.),Taqman® (Applied Biosystems, Foster City, Calif.) and Beadarrays™(Illumina, San Diego, Calif.).

Accordingly, the genetic markers of the present invention can be used inmarker-assisted selection methods to identify and/or select and/orproduce progeny having an Rps1 resistance allele. Such methods caninclude crossing a first soybean plant or germplasm with a secondsoybean plant or germplasm, wherein the first soybean plant or germplasmcomprises a SNP marker associated with an Rps1 resistance allele, andselecting a progeny plant that possesses the SNP marker. Therefore, inone embodiment of the present invention, a method of producing a soybeanplant having an Rps1 resistance allele is provided, the methodcomprising: (a) detecting, in a soybean germplasm, the presence of agenetic marker (SNPs or SNP combinations) associated with an Rps1resistance allele, wherein said marker comprises, consists essentiallyof, or consists of: (1) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ); (2) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(3) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ); (4) an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (5) an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (6) an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (7) an A allele at nucleotide 251 of SEQID NO:8 (SY2725AQ); (8) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:2 (SY2721AQ);(9) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a Gallele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (10) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ); (11) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), and a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(12) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), and a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (13) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (14) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (15) a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(16) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (17) wherein the SNPis an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an Aallele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (18) is a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (19) a G allele at nucleotide251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (20) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(21) an A allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (22) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (23) an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (24) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (25) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (26) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (27) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (28) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (29) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (30) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (31) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (32) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ), (33) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (34) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (36) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(37) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(39) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(41) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (46) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above; and (b) producing a soybean plantfrom said soybean germplasm, thereby producing a soybean plant havingthe Rps1 resistance allele.

In other embodiments, the present invention provides a method ofintrogressing an Rps1 resistance allele into a soybean germplasm that islacking the Rps1 resistance allele, the method comprising: (a) crossinga donor parental soybean line comprising a genetic marker associatedwith an Rps1 resistance allele with a recurrent parental soybean linethat lacks said marker to produce progeny; (b) selecting progenycomprising said marker and backcrossing said progeny with the recurrentparental soybean line, wherein said progeny are selected by detecting,in their genomes, the presence of the marker associated with an Rps1resistance allele, wherein the marker comprises: (1) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ); (2) a C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ); (3) a G allele at nucleotide 251 of SEQID NO:4 (SY2726BQ); (4) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ); (5) an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(6) an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (7) an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (8) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele at nucleotide251 of SEQ ID NO:2 (SY2721AQ); (9) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ) and a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ); (10) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (11) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), and a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (12) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), and a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(13) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (14) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (15) a C allele at nucleotide251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (16) a G allele at nucleotide 251 of SEQ ID NO:4(SY2726BQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(17) wherein the SNP is an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(18) is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (19) a G allele atnucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an A allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (20) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:6(SY2724BQ); (21) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (22) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (23) an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (24) an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (25) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (26) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (27) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (28) a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (29) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (30) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (31) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (32) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ), (33) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (34) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ),and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), (35) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (36) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(37) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (38) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(39) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (40) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(41) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (42) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (43) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (44) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (45) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (46) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (47) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (48) C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (49) an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (50) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (51) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (52) an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ; (53) an A alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (54) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), anA allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (55) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(56) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), (57) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (58) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (59) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination of (1)-(59) above; (c) backcrossing the selectedprogeny of (b) with the recurrent parental soybean line to producefurther progeny; and (d) repeating steps (b) to (c) one or more times(e.g., one, two, three, four, five, six, seven, eight, nine, ten, ormore times), thereby introgressing the Rps1 resistance allele into therecurrent parental line, and thus introgressing the Rps1 resistanceallele into the soybean germplasm that is lacking the Rps1 resistanceallele.

In some embodiments, a method for introgressing an Rps1 resistanceallele into a soybean germplasm lacking the Rps1 resistance allele,comprises: (a) crossing a plant identified, selected or producedaccording to any of the methods described herein with a second soybeanplant lacking the Rps1 resistance allele to produce a segregatingpopulation of plants; (b) screening the plants from the segregatingpopulation of (a) for the Rps1 resistance allele by detecting, in theplants from the segregating population, the presence of a genetic markerassociated with an Rps1 resistance allele as described herein; and (c)selecting a plant from (b) in which the genetic marker is detected,thereby introgressing an Rps1 resistance allele into the soybeangermplasm.

In other embodiments of this invention, a method of for producing aninbred soybean plant that is homozygous for an Rps1 resistance allele isprovided, the method comprising: (a) selecting a first donor parentalline having an Rps1 resistance allele by detecting, in the first donorparental line, a genetic marker associated with an Rps1 resistanceallele as described herein; (b) crossing the first donor parental linewith a second parental line in hybrid combination to produce asegregating plant population; (c) screening the plants from thesegregating population of (b) for the Rps1 resistance allele bydetecting, in the plants from the segregating population, the presenceof the genetic marker associated with an Rps1 resistance allele asdescribed herein; (d) selecting plants from the population of (c) havingthe genetic marker associated with an Rps1 resistance allele; and (e)screening the selected plants of (d) to identify an inbred soybean plantthat is homozygous for the Rps1 resistance allele, thereby producing aninbred soybean plant that is homozygous for the Rps1 resistance allele.

As described herein, the methods of the present invention encompassdetection of Rps1 alleles by detecting the presence of a genetic markerof this invention, wherein the Rps1 resistance alleles comprise Rps1-a,Rps1-c, and/or Rps1-k. Therefore, in some embodiments of this invention,methods of producing a soybean plant having an Rps1-a resistance alleleand/or an inbred soybean plant that is homozygous for an Rps1-aresistance allele and/or methods for introgressing an Rps1-a resistanceallele into a soybean germplasm lacking the Rps1-a resistance allele areprovided, wherein the step of detecting the presence of a genetic markerassociated with an Rps1-a resistance allele, comprises detecting thepresence of the marker comprising: (1) a T allele at nucleotide 251 ofSEQ ID NO:1 (SY2723AQ); (2) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:2 (SY2721AQ);(3) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a Gallele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ); (4) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ) and a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ); (5) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), and a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(6) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C alleleat nucleotide 251 of SEQ ID NO:5 (SY2726DQ), and a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (7) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ IDNO:3 (SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (8) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); or any combination thereof.

In other embodiments, the present invention provides methods ofproducing a soybean plant having an Rps1-c resistance allele and/or aninbred soybean plant that is homozygous for an Rps1-c resistance alleleand/or methods for introgressing an Rps1-c resistance allele into asoybean germplasm lacking the Rps1-c resistance allele, wherein the stepof detecting the presence of a genetic marker associated with an Rps1-cresistance allele, comprises detecting the presence of a genetic markercomprising: (1) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ);(2) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ); (3) an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ); (4) a C allele atnucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (5) a G allele at nucleotide 251 of SEQID NO:4 (SY2726BQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (6) wherein the SNP is an A allele at nucleotide 251 of SEQID NO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (7) is a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ) and an A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ);(8) a G allele at nucleotide 251 of SEQ ID NO:4 (SY2726BQ) and an Aallele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (9) an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide251 of SEQ ID NO:6 (SY2724BQ); (10) an A allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (11) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); or any combination thereof.

In further embodiments, the present invention provides methods ofproducing a soybean plant having an Rps1-k resistance allele and/or aninbred soybean plant that is homozygous for an Rps1-k resistance alleleand/or methods for introgressing an Rps1-k resistance allele into asoybean germplasm lacking the Rps1-k resistance allele, wherein the stepof detecting the presence of a genetic marker associated with an Rps1-kresistance allele, comprises detecting the presence of the geneticmarker comprising: (1) an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (2) an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ)and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (3) an Aallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:6 (SY2724BQ); (4) a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (5) a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ),a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (6) a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ IDNO:6 (SY2724BQ); (7) a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ); (8) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:7 (SY2724CQ); (9) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (10) a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQID NO:6 (SY2724BQ); (11) a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), an G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:6 (SY2724BQ), (12) an Aallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (13) an A allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ), (14) an A allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and a G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination thereof.

In additional embodiments, the present invention provides methods ofproducing a soybean plant having an Rps1-a resistance allele and anRps1-c resistance allele and/or an inbred soybean plant that ishomozygous for an Rps1-a resistance allele and an Rps1-c resistanceallele and/or methods for introgressing an Rps1-a resistance allele andan Rps1-c resistance allele into a soybean germplasm lacking the Rps1-aand Rps1-c resistance alleles, wherein the step of detecting thepresence of a genetic marker associated with an Rps1-a resistance alleleand an Rps1-c resistance allele, comprises detecting the presence of thegenetic marker comprising: (1) a T allele at nucleotide 251 of SEQ IDNO:1 (SY2723AQ) and a C allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ); (2) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ)and an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), (3) a Tallele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele at nucleotide 251of SEQ ID NO:8 (SY2725AQ), and an A allele at nucleotide 251 of SEQ IDNO:7 (SY2724CQ); (4) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a Gallele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); or any combination thereof.

In some embodiments, the present invention provides methods of producinga soybean plant having an Rps1-a resistance allele and an Rps1-kresistance allele and/or an inbred soybean plant that is homozygous foran Rps1-a resistance allele and an Rps1-k resistance allele and/ormethods for introgressing an Rps1-a resistance allele and an Rps1-kresistance allele into a soybean germplasm lacking the Rps1-a and Rps1-kresistance alleles, wherein the step of detecting the presence of agenetic marker associated with an Rps1-a resistance allele and an Rps1-kresistance allele, comprises detecting the presence of the geneticmarker comprising: (1) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ) and an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ);(2) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a G alleleat nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ); (3) a T allele at nucleotide251 of SEQ ID NO:1 (SY2723AQ), an C allele at nucleotide 251 of SEQ IDNO:5 (SY2726DQ) and an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ); (4) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a G allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (5) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a G allele at nucleotide 251 of SEQ ID NO:3(SY2724AQ), a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) andan A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (6) a T alleleat nucleotide 251 of SEQ ID NO:1 (SY2723AQ), a C allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ); (7) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), a G allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); (8) a T allele at nucleotide 251 of SEQID NO:1 (SY2723AQ), a C allele at nucleotide 251 of SEQ ID NO:5(SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ), anda G allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ); or anycombination thereof.

In some embodiments, the present invention provides methods of producinga soybean plant having an Rps1-c resistance allele and an Rps1-kresistance allele and/or an inbred soybean plant that is homozygous foran Rps1-c resistance allele and an Rps1-k resistance allele and/ormethods for introgressing an Rps1-c resistance allele and an Rps1-kresistance allele into a soybean germplasm lacking the Rps1-c and Rps1-kresistance alleles, wherein the step of detecting the presence of agenetic marker associated with an Rps1-c resistance allele and an Rps1-kresistance allele, comprises detecting the presence of the geneticmarker comprising: (a) an A allele at nucleotide 251 of SEQ ID NO:6(SY2724BQ); (b) an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(3) C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ); (4) an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ) and an A allele at nucleotide251 of SEQ ID NO:8 (SY2725AQ); (5) a C allele at nucleotide 251 of SEQID NO:3 (SY2724AQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(6) a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ), a G alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A allele atnucleotide 251 of SEQ ID NO:7 (SY2724CQ); (7) an A allele at nucleotide251 of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ) and an A allele at nucleotide 251 of SEQ ID NO:7(SY2724CQ; (8) an A allele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ),a G allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (9) an A allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);(10) an A allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ), an Aallele at nucleotide 251 of SEQ ID NO:5 (SY2726DQ), an A allele atnucleotide 251 of SEQ ID NO:8 (SY2725AQ), and a G allele at nucleotide251 of SEQ ID NO:7 (SY2724CQ); or any combination thereof.

In other embodiments, the present invention provides methods ofproducing a soybean plant having an Rps1-a resistance allele, an Rps1-cresistance allele and an Rps1-k resistance allele and/or an inbredsoybean plant that is homozygous for an Rps1-a resistance allele, anRps1-c resistance allele and an Rps1-k resistance allele and/or methodsfor introgressing an Rps1-a resistance allele, an Rps1-c resistanceallele and an Rps1-k resistance allele into a soybean germplasm lackingthe Rps1-a, Rps1-c, and Rps1-k resistance alleles, wherein the step ofdetecting the presence of a genetic marker associated with an Rps1-aresistance allele, an Rps1-c resistance allele and an Rps1-k resistanceallele, comprises detecting the presence of the genetic markercomprising: (1) a T allele at nucleotide 251 of SEQ ID NO:1 (SY2723AQ),a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ) and an A alleleat nucleotide 251 of SEQ ID NO:8 (SY2725AQ), (2) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), and an A allele at nucleotide 251 of SEQ IDNO:8 (SY2725AQ); (3) a T allele at nucleotide 251 of SEQ ID NO:1(SY2723AQ), is a C allele at nucleotide 251 of SEQ ID NO:3 (SY2724AQ),an A allele at nucleotide 251 of SEQ ID NO:8 (SY2725AQ) and an A alleleat nucleotide 251 of SEQ ID NO:7 (SY2724CQ); (4) a T allele atnucleotide 251 of SEQ ID NO:1 (SY2723AQ), an A allele at nucleotide 251of SEQ ID NO:5 (SY2726DQ), an A allele at nucleotide 251 of SEQ ID NO:8(SY2725AQ), and an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ);or any combination thereof.

Soybean Plants, Parts Thereof, and Germplasms Having Rps1 ResistanceAlleles

The present invention provides soybean plants and germplasms having Rps1resistance alleles (e.g., Rps1-a, Rps1-c, and/or Rps1-k) and resistanceto P. sojae. As discussed above, the methods of the present inventioncan be utilized to identify, produce and/or select a soybean plant orgermplasm having an Rps1 resistance allele. In addition to the methodsdescribed above, a soybean plant or germplasm having an Rps1 resistanceallele may be produced by any method whereby a marker associated with anRps1 resistance allele is introduced into the soybean plant or germplasmby such methods that include, but are not limited to, transformation(including, but not limited to, bacterial-mediated nucleic acid delivery(e.g., via Agrobacteria)), viral-mediated nucleic acid delivery, siliconcarbide or nucleic acid whisker-mediated nucleic acid delivery, liposomemediated nucleic acid delivery, microinjection, microparticlebombardment, electroporation, sonication, infiltration, PEG-mediatednucleic acid uptake, as well as any other electrical, chemical, physical(mechanical) and/or biological mechanism that results in theintroduction of nucleic acid into the plant cell, or any combinationthereof), protoplast transformation or fusion, a double haploidtechnique, embryo rescue, or by any other nucleic acid transfer system.

“Introducing” in the context of a plant cell, plant and/or plant partmeans contacting a nucleic acid molecule with the plant, plant part,and/or plant cell in such a manner that the nucleic acid molecule gainsaccess to the interior of the plant cell and/or a cell of the plantand/or plant part. Where more than one nucleic acid molecule is to beintroduced these nucleic acid molecules can be assembled as part of asingle polynucleotide or nucleic acid construct, or as separatepolynucleotide or nucleic acid constructs, and can be located on thesame or different nucleic acid constructs. Accordingly, thesepolynucleotides can be introduced into plant cells in a singletransformation event, in separate transformation events, or, e.g., aspart of a breeding protocol. Thus, the term “transformation” as usedherein refers to the introduction of a heterologous nucleic acid into acell.

Thus, a soybean plant, or part thereof, having an Rps1 resistance allele(i.e., P. sojae-resistant soybean plant or part thereof), obtainable bythe methods of the presently disclosed subject matter, are aspects ofthe presently disclosed subject matter. In some embodiments, the soybeanplant of the present invention has more than one Rps1 resistance alleleas described herein.

The soybean plant, or part thereof, of this invention having an Rps1resistance allele can be heterozygous or homozygous for the resistanceallele. In some embodiments of this invention, the soybean plant hasmore than one Rps1 resistance allele and thus, can be heterozygous atsome Rps1 resistance alleles and homozygous at other Rps1 resistancealleles.

The soybean plant or germplasm may be the progeny of a cross between avariety of soybean and a second variety of soybean that comprises anRps1 resistance allele.

The soybean plant or germplasm may be the progeny of an introgressionwherein the recurrent parent is a variety of soybean and the donorcomprises an Rps1 resistance allele.

The soybean plant or germplasm may be the progeny of a cross between afirst variety of soybean (e.g., a tester line) and the progeny of across between a second variety of soybean (e.g., a recurrent parent) anda variety of soybean that comprises an Rps1 resistance allele (e.g., adonor).

The soybean plant or germplasm may be the progeny of a cross between afirst variety of soybean and the progeny of an introgression wherein therecurrent parent is a second variety of soybean and the donor comprisesan Rps1 resistance allele.

Another aspect of the presently disclosed subject matter relates to amethod of producing seeds that can be grown into P. sojae-resistantsoybean plants. In some embodiments, the method comprises providing a P.sojae-resistant soybean plant of this invention, crossing the P.sojae-resistant plant with another soybean plant, and collecting seedsresulting from the cross, which when planted, produce P. sojae-resistantsoybean plants.

Accordingly, the present invention provides improved soybean plants,seeds, and/or tissue cultures produced by the methods described herein.In further embodiments, the present invention provides introgressedGlycine max plants and/or germplasm produced by the methods describedherein.

Compositions for Analysis of a Soybean Genome

In some embodiments, the presently disclosed subject matter providesmethods for analyzing the genomes of soybean plants/germplasms toidentify those that include desired markers associated with P. sojaeresistance. In some embodiments, the methods of analysis compriseamplifying subsequences of the genomes of the soybean plants/germplasmsand determining the nucleotides present in one, some, or all positionsof the amplified subsequences.

Thus, in some embodiments, the present invention provides compositionscomprising one or more amplification primer pairs capable of initiatingDNA polymerization by a DNA polymerase on a Glycine max nucleic acidtemplate to generate a Glycine max marker amplicon. In some embodiments,the Glycine max amplicon can be used to identify the Glycine max markercomprising a nucleotide sequence of any of SEQ ID NOs: 1-8. In view ofthe disclosure of SEQ ID NOs: 1-8 as being linked to pathogen resistanceloci, one of ordinary skill in the art would be aware of varioustechniques that could be employed to analyze the sequences of thecorresponding soybean nucleic acids. Representative amplification primerpairs can comprise the nucleotide sequences of a forward primer andcorresponding reverse primer as set forth hereinabove in Table 1.

The following examples are included to demonstrate various embodimentsof the invention and are not intended to be a detailed catalog of allthe different ways in which the present invention may be implemented orof all the features that may be added to the present invention. Personsskilled in the art will appreciate that numerous variations andadditions to the various embodiments may be made without departing fromthe present invention. Hence, the following descriptions are intended toillustrate some particular embodiments of the invention, and not toexhaustively specify all permutations, combinations and variationsthereof.

EXAMPLES Example 1 Soybean Lines

To determine and validate the accuracy of the eight SNP markers (setforth in Table 1) for detecting the Rps-1 resistance alleles, Rps1a,Rps1c, Rps1k, and susceptible allele, 337 Syngenta soybean lines wereselected. Among the 337 lines, 82 lines carry Rps1a, 82 lines containRps1c, 81 lines have Rps1k, and 92 lines are susceptible to P. sojae(see, Table 2).

Example 2 Screening for Phytopthora Sojae Resistance in Soybean

Zoospores of P. sojae were obtained by transferring peripheral disksfrom young colonies (3-4 days old) to a new plate and incubating themfor 24 h at 21° C. with intermittent washings (3-4 washes or as needed)with sterilized distilled water to promote sporangia production. Afterovernight incubation zoospores were released from sporangia that arecollected, counted in hemacytometer, and diluted to the requiredconcentration.

Four inch square pots filled with vermiculate were planted with 20soybean seeds, which are allowed to germinate. Young seedlings ofsoybean (5-7 days old) were inoculated with 20,000 zoospres/ml usingsyringe (30G) by making a slit in the hypocotyls of the plant andplacing a droplet of the zoospore suspension. Seedlings were incubatedin a growth chamber at 21° C. for about 7 days post inoculation under12-14 h light and then moved to greenhouse and maintained at 24° C. with12-14 h light conditions for another 3-5 days before rating for disease.Susceptible (hosts) plants develop distinctive symptoms and died 3-5days after inoculation. Resistant (non-host) plants develophypersensitive reaction and the symptom development fails to progressbeyond the site of inoculation. Less than 25% of the plants that diefrom P. sojae are resistant; 26 to 75% of the plants that die areintermediate in resistance; and greater than 75% of the plants that diefrom P. sojae infection are susceptible. An intermediate reaction caneither indicate contamination of the soybean line or a mixed culture ofthe pathotype. Respective differential checks are used as controls tovalidate the purity of the pathotype. The Rps1 resistance alleles 1a,1c, 1k and susceptible rps1 in soybean lines were determined based onhost-pathogen interactions as shown in Table 3, below. Using thismethod, the Rps1 alleles in 337 soybean lines were identified, whichwere selected for further research (See, e.g., Table 1).

TABLE 3 Response of different P. sojae races to Rps1 resistance alleles.P. sojae races (pathotypes) gene (s) 1 2 3 4 7 25 31 OH8 Rps1a R R S S SS R R Rps1c R R R S R S R R Rps1k R R R R R S S R Susceptible rps1 S S SS S S S S

Example 3 SNP Genotyping

The tissue from each soybean line was obtained by growing the plants inthe field or greenhouse. DNA was extracted from the leaf tissue of 7-10day old seedlings (7-10 days after planting). DNA can be extracted fromplant tissue in any way known in the art, including the CTAB(hexadecyltrimethylammonium bromide) method (See, e.g., Stewart et al.,BioTechniques 14(5):748-749 (1993)), sodium hydroxide, and theDellaporta method (Dellaporta et al., Plant Mol. Biol. Rep. 1:19-21(1983)). Additional art known methods of DNA extraction also can be used(See, e.g., Sambrook & Russell Molecular Cloning: A Laboratory Manual,Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., United States of America (2001)). DNA is diluted in TE buffer andstored at 4° C. for use in PCR reactions as described below in Table 4.

TABLE 4 PCR was set up in 5 μl final volumes according to the followingformula. Per For 96 Stock reaction samples Final Reagent concentration(μl) (μl) concentration 2X Master Mix (JumpStart ™  2X 2.5 296.88   1XTaq ReadyMix ™) AbD primer/probe mix (80x) 40x .0625 6 0.5x PCR-qualityH2O — 2.44 234.24 — DNA (dried in 384) 4.5 ng/μl 4 — 3.6 ng/ul (18 ng)Final Volume (ul) 5.00 357.44

The Master Mix is JumpStart™ Taq ReadyMix™ (Sigma Catologue No. 2893;Sigma Chemical Co., St. Louis, Mo., United States of America), a premixof all the components, including nucleotides and Taq polymerase (notincluding the primers or probes) necessary to perform a 5′-nucleaseassay. Before use, 1375 μl of 1.0 M MgCl₂ (Sigma Catalogue No. M1028)and 250 μl of 300 μM Sulforhodamine 101 (Sigma Catalogue No. S7635),also known as ROX, are added to a 125 mL bottle of JumpStart™ TaqReadyMix™. PCR plates were placed in an ABI 9700 thermal cycler and theprogram set forth in Table 5 was run:

TABLE 5 PCR program. Task SNP1 Initial denaturation 50° C. for 2 min;followed by 95° C. for 10 min Cycles 95° C. for 15 sec 60° C. for 1 minNumber of cycles 40 Final elongation 72° C. for 5 min Hold Hold at 4° C.

The ABI 7900 Sequence Detection System (or Taqman®) was used tovisualize the results of an allelic discrimination (SNP) assay. Usingthe Sequence Detection System (SDS) software, allele calls were madebased on the fluorescence for the two dyes measured in each sample.

Example 4 Validation of SNP Markers for Rps1a, Rps1c, Rps1k, andSusceptible Allele in Soybean

The eight SNP markers as shown in Table 1 were validated for the Rps1-a,Rps1-c, Rps1-1k, and/or susceptible allele in 337 soybean lines. Theresults are set forth in Table 6 and confirmed the phenotypic data(Example 4).

TABLE 6 Validation of eight SNP markers for Rps1a, Rps1c, Rps1k, andsusceptible allele in 337 soybean lines. Rps1 SY2723AQ SY2721AQ SY2724AQSY2726BQ SY2726DQ SY2724BQ SY2724CQ SY2725AQ Soybean Line allele (A/T)(A/C) (C/G) (C/G) (A/C) (A/G) (A/G) (A/G) AR0800164 1A T A G C C G G GNE0800402 1A T C G C C G G G BK0800608 1A T C G C C G G G S48-C9 1A T CG — H G — G BN0810632 1A T C G C C G G G BN0810574 1A T C G C C G G GOW0810225 1A T C G C C G G G OW0810227 1A T C G C C G G G OW0810261 1A TC G C C G G G OW0810211 1A T C G C C G G G NE0800396 1A T C G C C G G GNE0800405 1A T A G C C G G G NE0800408 1A T A G C C G G G NE0800447 1A TC G C C G G G NE0800450 1A T C G C C G G G NE0800452 1A T C G C C G G GWN0810484 1A T C G C C G G G XR3201 1A T C G C C G G G WN0800538 1A T CG C C G G G WN0800547 1A T C G C C G G G WN0800570 1A T C G C C G G GWN0800576 1A T C G C C G G G BK0810186 1A T C G C C G G G HI0810776 1A TC G C C G G G NE0810334 1A T H G C C G G G S19-V2 1A T C G C C G G GOW0810298 1A T C G C C G G G GO0800735 1A T C G C C G G G SJ0800051 1A TC G C C G G G WN0810620 1A T C G C C G G G BN0810584 1A T C G C C G G GSJ0800206 1A T C G C C G G G SJ0810655 1A T C G C C G G G WN0810659 1A TC G C C G G G WN0810614 1A T C G C C G G G WN0800534 1A T C G C C G G GWN0800539 1A T C G C C G G G WN0800556 1A T C G C — G G G WN0800558 1A TC G C C G G G WN0800564 1A T C G C C G G G HI0800661 1A T H G C C G G GBY0810791 1A T C G C C G G G SJ0810773 1A T C G C C G G G SJ0810828 1A TC G C C G G G HI0810825 1A T C G C C G G G HI0810742 1A T C G C C G G GXR4317 1A T C G C C G G G BN0800121 1A T C G C C G G G HI0800685 1A T CG C C G G G S10-K1 1A T C G C C G G G S00-W3 1A T A G C C G G G S15-B11A T C G H H G — G S21-H3 1A T C G C C G G G S36-B6 1A T C G C C G G GS30-D4 1A T C G C C G G G S23-N7 1A T C G C C G G G S34-R2 1A T C G C CG G G S30-F5 1A T C G C C G G G S31-H9 1A T C G C C G G G S33-K5 1A T CG C C G G G SJ0800048 1A T C G C C G G G SJ0800052 1A T C G C C G G GXR3192 1A T C G C C G G G SJ0800227 1A T C G C C G G G SJ0800213 1A T CG C C G G G HI0800614 1A T C G C C G G G SJ0800047 1A T A G C C G G GSJ0810784 1A T C G C — G G G BN0810737 1A T C G C C G G G S23-H2 1A T CG C C G G G S25-B9 1A T C G C C G G G S27-L4 1A T C G C C G G G S29-J61A T C G C C G G G S19-R5 1A T C G C C G G G S00-A6 1A T C G C C G G GS23-Z3 1A T C G C C G G G S28-G1 1A T C G C C G G G S22-F5 1A T C G C CG G G S32-E2 1A T C G C C G G G S00-Z1 1A T A G C C G G G BN0810573 1A TC G C C G G G BN0810700 1A T C G C C G G G S36-J4 1C A C C G A A A GXR1707 1C A C C G A A A G AR0800193 1C A A C G A A A G WW221162 1C A C CG A A A G OW0800388 1C A C C G A A A G S02-M9 1C A C C G A A A G05BR047009 1C A C C G A A A G BN0810695 1C A C C G A A A G BN0810688 1CA C C G A A A G BN0810641 1C A C C G A A A G S49-F4 1C A C C G A — A GS51-T8 1C A C C G — A A G S50-N3 1C A H C H A — A G S54-G9 1C A C C G AA A G S49-T1 1C A C C G A A A G S10-B7 1C A C C G A A A G XR0790 1C A CC G A A A G OW0810046 1C A C C G A — — G GO0810012 1C A C C G A A A GGO0810004 1C A C C G A A A G GO0810013 1C A C C G A A A G GO0810083 1C AC C G A A A G S00-J9 1C A C C G A A A G GO0810108 1C A C C G A A A GBK0810126 1C A C C G A A A G OW0810085 1C A A C G A A A G S00-H7 1C A CC G A A A G XR0304 1C A C C G A A A G S04-Z9 1C A C C G A A A G S08-C31C A C C G A A A G XR0202 1C A C C G A A A G BN0810836 1C A C C G A — AG HI0810829 1C A C C G A A A G HI0810818 1C A C C G — — A G HI0810800 1CA C C G A A A G HI0810826 1C A C C G A A A G HI0810830 1C A C C G A A AG HI0810831 1C A C C G A — A G HI0810837 1C A C C G A A A G HI0810819 1CA H C H — H A G S05-T6 1C A C C G A A A G S20-G7 1C A C C G A A A GS17-B5 1C A C C G A A A G S08-A2 1C A C C G A A A G S09-N6 1C A C C G AA A G S15-R2 1C A C C G A A A G S11-L2 1C A C C G A A A G S14-A7 1C A CC G A A A G S16-C4 1C A C C G A A A G S14-K6 1C A C C G A A A G S17-P91C A C C G A A A G S13-Y3 1C A C C G A A A G S03-B2 1C A A H G A A A GS12-P4 1C A C C G A A A G S12-C2 1C A C C G A — A G S21-V9 1C A C C G AA A G S44-J5 1C A C C G A A A G S47-D9 1C A C C G A A A G S43-N6 1C A CC G A A A G S46-U6 1C A C C G A A A G S33-T4 1C A C C G A A A G S44-D51C A C C G A A A G S23-T5 1C A C C G A A A G S22-C5 1C A C C G A A A GS38-H8 1C A C C G A A A G BN0800119 1C A C C G A A A G SJ0800222 1C A CC G A A A G S49-Q9 1C A C C G A A A G S06-D9 1C A C C G A A A G S01-T51C A C C G A A A G S38-T8 1C A C C G A A A G S35-F9 1C A C C G A A A GS39-Q4 1C A C C G A A A G S21-D2 1C A C C G A A A G S36-C7 1C A C C G AA A G S38-D5 1C A C C G A A A G NK 35-00 RR 1C A C C G A A A G S37-N4 1CA C C G A A A G S34-U4 1C A C C G A A A G S43-B1 1C A C C G A A A GS28-Y2 1C A C C G A A A G S30-J8 1C A C C G A A A G AR0800190 1K A A G CH A A A OW0800382 1K A A G C C A A A S14-N1 1K A A G C C A A A S29-W7 1KA A G C C A A A WN0810530 1K A A G C C A A A XR1892 1K A A G C C A A ANE0800095 1K A A G C C A A A S23-A8 1K A A G C C A A A BN0810534 1K A AG C C A A A BN0810542 1K A A G C C A A A OW0810238 1K A A G C C A A AOW0810183 1K A A G G A A A G OW0800371 1K A A G C C A A A OW0800373 1K AA G C C A A A OW0800366 1K A A G C C A A A 03JR101916 1K A A G C C A A ABN0810711 1K A C C G A A A G SJ0810677 1K A A G C C A A A SJ0810678 1K AA G C C A A A SJ0810705 1K A A G C C A A A HI0800665 1K A C C G A A A GHI0800672 1K A A G C C A A A HI0800688 1K A A G C C A A A HI0810907 1K AA G C C A A A S01-C9 1K A A G C C — A A S02-K3 1K A A G C C A A A S25-R31K A A G C C A A A OW0800083 1K A A G C C A A A XR00991 1K A A C G A A AG OW0800367 1K A A G C C A A A OW0800372 1K A A G C C A A A GO0810084 1KA A G C C A A A 03JR313108 1K A A G C C A A A 03KL015751 1K A A G C C AA A BN0810811 1K A A G C C A A A HI0810846 1K A H C H A A A — HI08108901K A A G C C A A A HI0800643 1K A A G C C A A A HI0800690 1K A A G C C AA A HI0800674 1K A A G C C A A A HI0800675 1K A A G C C A A A HI08006911K A A G C C A A A S14-C5 1K A A G C C A A A S13-K2 1K A A G C C — — AS13-A4 1K A A G C C A A A S11-J8 1K A A G C C A A A S21-N6 1K A C C G AA A G S13-J9 1K A C G C C A A A S11-R6 1K A A G C C A A A S23-C2 1K A AG C C A A A S10-T1 1K A A G H H A A — S45-E5 1K A A G C C A A A S28-B41K A A G C C A A A S24-J1 1K A A G C C A A A S27-C4 1K A A G C C A A AS32-N9 1K A A G C C A A A S26-P1 1K A A G C C A A A XR3493 1K A A G C CA A A SJ0810631 1K A A G C C A A A SJ0800018 1K A A G C C A A ANE0800088 1K A A G C C A A A WN0800106 1K A A G C C A A A BN0810561 1K AA G C C A A A HI0800667 1K A A G C C — A A HI0800677 1K A C C G A A A GHI0800682 1K A A G C C A A A HI0810765 1K A A G C C A A A HI0810713 1K AA G C C A A A BN0810753 1K A C C G A A A G BN0810745 1K A C C G A A A GBN0810788 1K A A G C C A A A BN0810767 1K A A G C C A A A SJ833009 1K AA G C C A A A S28-E6 1K A A — C C A A A S34-K1 1K A A G C C A A A S24-K61K A A G C C A A A XR3090 1K A A G C C A A A XR3191 1K A A G C C A A AXR4090 1K A A G C C A A A XR2090 1K A A G C C A A A S12-U7 1K A A G C CA A A BN0810762 SUSC A A G C C G G G BN0810763 SUSC A A G C C G G GBY0811028 SUSC A A G C C G G G OW0800357 SUSC A A G C C G G G HI0810916SUSC A A G C C G G G HI0810801 SUSC A A G C C G G G 03RM893031 SUSC A AG C C G — — SJ0800026 SUSC A A G C C G G G SJ0800032 SUSC A A G C C G GG WN0800102 SUSC A A G C C G G G BN0810627 SUSC A A G C C G G GBN0810673 SUSC A A G C C G G G BN0810653 SUSC A A G H H G — G SJ0800208SUSC A A G C C G G G SJ0810679 SUSC A A G C C G G — SJ0810611 SUSC A A GC C G G G HI0800616 SUSC A A G C C G G G HI0800650 SUSC T A G C C G G GHI0800662 SUSC T A G C C G G G HI0800669 SUSC A A G C C G G G BY0810934SUSC A A G C C G G G BY0810924 SUSC A A G C C G G G BY0810920 SUSC A A GC C G G G BY0810956 SUSC A A G C C G G G BY0810900 SUSC A A G C C G G GBY0810925 SUSC A A G H H G — G BY0810865 SUSC A A G C C G G G BY0810951SUSC A A G C C G G G BY0810999 SUSC A A G C C G G G BY0810908 SUSC A A GC C G G G BY0810913 SUSC A A G C C G G G BY0810930 SUSC A A G C C G G GBY0810946 SUSC A A G C C G G G BY0810857 SUSC A A G C C G G G BY0810887SUSC A A G — — G G G BY0811062 SUSC A A G C C G G G HI0810954 SUSC A A GC C G G G OW0800338 SUSC A A G C C G G G OW0800341 SUSC A A G C C G G GBN0810797 SUSC A A G C C G G G BY0810850 SUSC A A G — H G — G HI0800617SUSC A A G C C G G G HI0800621 SUSC A A G C C G G G HI0800624 SUSC A A GC C G G — HI0800625 SUSC A A G C C G G G HI0800626 SUSC A A G C C G G GHI0810803 SUSC A A G C C G G G HI0810795 SUSC A A G C C G G G HI0810775SUSC T A G C C G G G HI0810841 SUSC A A G C C G G G HI0800666 SUSC T A GC C G G G HI0800687 SUSC A A G C C G G G HI0800613 SUSC A A G C C G G GHI0800637 SUSC T A G C C G G G HI0800630 SUSC A A G C C G G G HI0800620SUSC A A G C C G G G HI0800619 SUSC A A G C C G G G HI0800670 SUSC T H GC C G G G HI0800618 SUSC T A G C C G G G SJ0810651 SUSC T A G C C G G GS12-B3 SUSC A A G C C G G G S12-T8 SUSC A A G C C G G G S08-M8 SUSC A AG C C G G G S35-T9 SUSC A A G C C G G G BN0810666 SUSC A A G C C G G GBN0800008 SUSC A A G C C G G G SJ0800020 SUSC A A G C C G G G OW0800084SUSC A A G C C G G G WN0800100 SUSC A A G C C G G G BN0810560 SUSC A A GC C G G G BN0810633 SUSC A A G C C G G G BN0800118 SUSC A A G C C G G GHI0800631 SUSC A A G C C G G G HI0800636 SUSC A A G C C G G G HI0800638SUSC A A G C C G G G HI0810743 SUSC A A G C C G G G HI0800647 SUSC T A GC C G G G HI0800651 SUSC T A G C C G G G HI0800652 SUSC A A G C C G G GHI0800657 SUSC T A G C C G G G BN0810790 SUSC A A G C C G G G BN0810768SUSC A A G C C G G G BN0810730 SUSC A A G C C G G G HI0810782 SUSC A A G— H G G G HI0810786 SUSC A A G C C G G G HI0810714 SUSC A A G C C G G GHI0800628 SUSC A A G C C G G G HI0800629 SUSC H A G C C G G G HI0800654SUSC A A G C C G G G NE0810532 SUSC H A G C C G G G XR3494 SUSC H A G CC G G G WN0800098 SUSC A A G C C G G G

The above examples clearly illustrate the advantages of the invention.Although the present invention has been described with reference tospecific details of certain embodiments thereof, it is not intended thatsuch details should be regarded as limitations upon the scope of theinvention except as and to the extent that they are included in theaccompanying claims.

Throughout this application, various patents, patent publications andnon-patent publications are referenced. The disclosures of thesepatents, patent publications and non-patent publications in theirentireties are incorporated by reference herein into this application inorder to more fully describe the state of the art to which thisinvention pertains.

That which is claimed:
 1. A method of producing a Glycine max plant thathas improved resistance to Phytophthora as compared to a control plant,the method comprising the steps of: (a) isolating a nucleic acid from aGlycine max plant; (b) detecting in the nucleic acid of (a) the presenceof a genetic marker that is associated with improved resistance toPhytophthora and is associated with Rps1c, wherein said genetic markercomprises SY2726DQ (SEQ ID NO: 5) and further comprises an A allele atnucleotide 251 of SEQ ID NO:5 (SY2726DQ) or is a genetic marker linkedthereto, wherein said genetic marker linked thereto comprises at leastone of an A allele at nucleotide 251 of SEQ ID NO: 1 (SY2723AQ), a Callele at nucleotide 251 of SEQ ID NO: 3 (SY2724AQ), a G allele atnucleotide 251 of SEQ ID NO: 4 (SY2726BQ), an A allele at nucleotide 251of SEQ ID NO: 6 (SY2724BQ), an A allele at nucleotide 251 of SEQ ID NO:7 (SY2724CQ), and a G allele at nucleotide 251 of SEQ ID NO: 8(SY2725AQ); (c) selecting a first Glycine max plant based on thepresence of the marker associated with improved resistance toPhytophthora in (b); (d) crossing a second Glycine max plant with thefirst Glycine max plant of (c) wherein, said second Glycine max plantdoes not comprise in its genome the marker associated with improvedresistance to Phytophthora in (c); (e) producing seed from the crossingof (d); and (f) selecting a Glycine max plant, grown from the seed of(e), that has improved resistance to Phytophthora and comprises thegenetic marker associated with improved resistance to Phytophthora andassociated with Rps1c.
 2. The method of claim 1, wherein Phytophthora isPhytophthora sojae.
 3. The method of claim 1, wherein the detectingcomprises detecting the presence of the genetic marker comprising the Aallele at nucleotide 251 of SEQ ID NO: 5 or an allelic form of saidgenetic marker linked thereto.
 4. The method of claim 1, wherein thesecond Glycine max plant is an elite soybean line.
 5. The method ofclaim 1, wherein the second Glycine max plant displays less resistanceto Phytophthora as compared to the first Glycine max plant.
 6. Themethod of claim 1 further comprising the step of backcrossing the plantsproduced in (e).